The Collective
by TV Manic 2
Summary: An explosion rocks Atlantis with Sheppard caught in the middle, but that's only the beginning of his day-off from hell. Something is loose in the city, and it's using the residents to reach its goal: total domination. Shepwhump fest, Sheyla - NOW COMPLETE
1. Concussed and Confused

**Stargate Atlantis -:- The Collective**

**Summary: **

An explosion rocks Atlantis with Sheppard caught in the middle, but that's only the beginning of his day-off from hell. Something is loose in the city, and it's using the residents to reach its goal: total domination. Shep-whump fest, implied Sheyla.

**Setting/Spoilers:**

Late Season 5, potential spoilers for any episode really

**Genre/Rating:**

Hurt/Comfort/Friendship/Action/Adventure – rated T to be safe

**Author's Note(s):**

Finally decided to take the plunge and start writing this fic; I will warn you though, that it really is still stuck in the planning stage – I've created an impossible situation, and at this point I have no idea how they get out of it – I'm going to try organic writing and see how it goes lol

On another note, this fic has a non-linear plotline with a lot of time-shifts between past and present (think 'Tabula Rasa' – great episode and inspiration for this fic) Keep an eye on the subtitles, in paticular the times, if it gets confusing – that's what I'm going to be doing :P

Okay, I think I'm done filling my word count now – Enjoy!

* * *

><p><strong>Chapter One -:- Concussed and Confused<strong>

**(Present) 11.00am – Central Tower/Laboratory Delta29-B**

Harsh light flashed against his eye-lids, easily convincing him to keep them closed. John Sheppard had hit his head enough times in the past to know that opening your eyes to bright light hurt like a son of a bitch. Even more so than the current pain that bounced around his skull like a rabbit armed with a jackhammer. He decided to try and figure out what was going on by ear instead.

After a moment of concussion-induced fogginess, he recognised the sound of sparking electrical cables – explaining the strange light flashes. You knew you had spent way too much time with Rodney McKay when you could actually identify the sound of shorting wiring. The thought of being that close to live electrics freaked him a little, but moving didn't seem like a good idea at that moment. He shifted slightly regardless only to find that he couldn't move anyway. Something heavy lay across his chest, the movement causing pain to flare up in his ribs.

Then he heard voices. They sounded miles away, but again by experience he knew them to be much closer. He couldn't make out what they were saying, but one sounded familiar and female while the other was totally foreign and male. They were coming closer, the garbled voices making intermittent sense.

"…a survivor…thrown…blast…"

"…the Voice decrees…taken…others?"

"…dead…only one…"

_What the hell?_ John was majorly confused. He began to panic a little when he realised he couldn't remember where he was or how he got there. There had been a 'blast' so…an explosion? That would explain the shorting wiring and the major headache he was now experiencing, but what was 'the Voice'? Who were the 'others'? Was he the only 'survivor'?

John got a little fed up of trying to piece things together with his eyes closed. Cautiously, he blinked them open, to find himself in a familiar room lit with emergency lights and sparks. He recognised the décor as Atlantean, reassuring him, if only a little, that he was likely still in Atlantis. He turned his head slightly, a blurred figure coming into view above him. "K-Keller?"

Dr. Jennifer Keller didn't react to her name at all. She wasn't even looking at him, instead staring intently at the tablet PC attached to the medical scanner she was currently waving over him. A look of annoyance flickered across her features and she addressed the unknown male that John couldn't see. "He is not of the Infected."

"We have located another potential threat to The Collective," the other person replied. John tried to process what he was hearing, but nothing was making sense. "He is wearing the dress of the Civilian class. He has been assessed as a low threat level. The Voice decrees that he be contained."

John briefly wondered if they were definitely talking about him or not – he was rarely ever seen in anything other than his BDUs, but the guy had claimed he was wearing civvies. It was then that he felt the unfamiliar denim material on his legs, confirming that he was wearing jeans. He must've been off-duty when whatever happened, happened. Apparently in typical Sheppard-style he had managed to find trouble even on his day-off.

The weight across his midsection abruptly disappeared as someone outside of his field of vision lifted off the rubble pinning him. John gratefully took a deep breath, but instantly regretted it when the action set his lungs on fire. Two others dressed in the Lantis military uniform loomed into view, but they were new recruits that John had yet to learn the names of. They each grabbed one of his arms and hauled him to his feet; the pain of his injuries nearly causing him to pass out.

Now upright, John got a better view of the destruction around him. He could make out enough of the damage through blurring vision to know that it had been one helluvan explosion – he was lucky to have survived with only the _relatively_ minor injuries he had. He caught a glimpse of a charred hand poking out from behind the remains of a console as the soldiers dragged him out of the room. John panicked when he realised that he had no idea who the hand belonged to – who had been in the room with him? What were they even doing in there in the first place? What the hell had happened; and what the hell was going on now?

Stepping out into the corridor beyond didn't help ease his confusion. At the door stood four more soldiers, all heavily armed and kitted out in full assault gear. They didn't acknowledge the presence of Sheppard's entourage, but silently stepped aside as they passed. John noted the heavy guard, filing the information away for later. Once in the hallway Keller led them down and to the left. They passed through two more corridors and took a transporter trip before John finally realised where they were going. The holding cell.

He was going to blame the slow realisation and his complete lack of direction on the concussion. It had stolen that along with his memory and his ability to move unaided.

From the transporter they stepped into a corridor full of activity. Atlantis personnel streamed purposefully up and down the hall; all of them completely oblivious to John's captivity. Sheppard blinked in confusion, wondering if he was even more concussed than he was taking credit for and was imagining the whole thing. The scene around him was just so normal it didn't fit with the wacky weirdness he had woken to. It wasn't until he took a closer look that he realised that there was nothing 'normal' about the people milling around him.

Their eyes were completely glazed over and unseeing; although their steps were sure as if they weren't being guided by mere vision. There was no noise either; none of the usual chatting or hailing – just the practically robotic march of booted feet echoing around the space. John immediately drew the similarity to a Replicator-controlled Atlantis and shuddered. God, he really hoped that wasn't what was happening.

As they continued down the hall, literally two corridors away from the cell, John was disheartened to see so many familiar faces completely ignoring him. A lot of the people passing were his own men, fully cladded out in tactical gear, P90s held ready at their chests. The others were scientists and civilians who were also armed, but only trusted with Wraith stunner pistols. It appeared that whatever hierarchy previously occurred still existed – though the soldiers now seemed more willing to do as the geeks ordered.

They turned a corner, and hope bloomed in Sheppard's battered rib-cage. "T-Teyla."

The Athosian ignored him; eyes front as she approached – her path aiming to take her around the parade surrounding him. He called out louder, even as he realised it was hopeless to reach her through whatever control had taken over. Surprisingly, she stopped; as did the soldiers gripping his arms and Keller who was leading. Apparently, Teyla held a higher rank than those arresting him, and everyone else too as absolutely everything came to an eerie stop.

Once again, John flashed to a memory of the Replicators rendered stationary by McKay's computer program. If it weren't for the fact he could see the slight flicker of their eyelids, he would've sworn that everyone had been flash frozen. He considered using the opportunity to escape, but the grip on his arms had also frozen like a vice.

Then Teyla spoke; but the words didn't sound like her at all. "New memory data received. The prisoner is of Military class; rank Lieutenant Colonel. Threat level re-assessment complete. The prisoner is a danger to The Collective. The Voice decrees that he is to be terminated."

With barely a flicker of movement, John found the business end of a 9mm handgun in his face. "Now?"

Teyla ignored his comment; though the empty click of her thumbing the hammer down answered his question.

This was turning out to be one helluva day-off.

* * *

><p><strong>(Past) 08.00am – Central TowerMess Hall **

"Aren't you up a little early on your day-off?"

John looked up at the owner of the voice only to see a piled-high tray of breakfast goodies. That alone told him that Rodney McKay had arrived. The astrophysicist took the seat opposite him and rubbed his hands in barely contained glee at the feast before him. John glanced at his own forgotten half-eaten breakfast then shrugged. "I am physically incapable of sleeping past 5.53 in the morning." He answered and Rodney gave him a curious look. "A trauma from way back at Basic that I have no desire to revisit."

Rodney gave a snort as a reply, his mouth already occupied with a way too larger bite of food. John returned his attention to the tablet PC he had hijacked to complete the last-minute paperwork he was meant to have done the day before. So far he had managed to avoid Woolsey and the inevitable lecture about bureaucracy that would follow, but he knew his luck would run out eventually. Rodney slowly managed to chew and swallow his first mouthful. He jabbed his fork at John "Didn't know you owned anything other than your uniform and a closet of black t-shirts."

"Me neither," John answered, giving his outfit a glance. He had honestly been stumped that morning when he realised that he had to pick something other than his uniform to wear. He had managed to find a pair of jeans, a t-shirt and a black shirt after searching his yard-sale of a room. "Found it in the duffle I still haven't unpacked since I took leave last year."

Rodney rolled his eyes and proceeded to shovel another monumental bite of food in his mouth. Ronon and Teyla took that opportunity to arrive, each taking their seats without a word. This had been 'their' table for nearly four years now; their routine set in stone. Teyla gave Rodney an inquisitive look as she watched him struggle to chew his mouthful, then gave a small sigh as Ronon took it as a challenge and spooned in an even larger amount. Honestly, neither of them would ever learn proper table manners. She then looked at John who was still stabbing at the computer. "I thought it was your day-off?"

"So did I," John smirked as he managed to type on the tiny touch keyboard. The computer gave a congratulatory beep, and John gave her his most charming smile as he laid it down. "And now it is. God forbid I file a mission report more than a day late."

"Considering our last mission was nearly a fortnight ago, I would say it was little more than 'a day' late," Teyla gently chastised. John just shrugged.

"By my standards – this was early," he closed the file he was working on and opened a game of solitaire. Teyla had never really understood the game, but she often found the Lantis personnel playing it when they believed their superiors weren't looking. Apparently there was a competition going on where players published their scores online – Rodney was still sore over John topping his high score. Without looking up, he picked up on the one person missing from the table. "Where's Torren?"

Teyla smiled like she always did whenever she thought of her son. "Dr. Keller wanted to spend some time with him before he goes to New Athos this afternoon. Kanaan is expecting us after noon."

Teyla didn't miss the slight shift in emotion on John's face, although the two men having the eating contest opposite obviously did. She never knew what to make of the odd expression he had whenever she mentioned Kanaan; it was usually gone the same instant it appeared. Some small part of her hoped it was jealousy – had he finally realised that there was something more than mutual respect between the two of them? In all the years she had known John, the only time he had ever made a move was when he was under the influence of the iratus retrovirus. Truthfully, she had never made a move either, but that was the way of her people.

It was too late now anyway. Even thouugh the relationship between her and Kanaan had been strained by the distance between them; they had a son, and Teyla would always do what was best for Torren.

The look was gone now, John's typical cavalier expression propped back in place. He was still focused on his card game, his eyes never meeting hers. Teyla briefly wondered if he was distancing himself from her on purpose; his respect for her outweighing any other feelings he may have. The logical part of her was grateful. If either of them acted on feelings neither would admit, she doubted she would be ready for the complications that would follow.

The silence was broken my Ronon's celebratory cheer. McKay threw him a look over reddened cheeks as he spluttered slightly. As it turned out, the unspoken rule of the challenge was that the victor was the one who ate the fastest without choking. Rodney, having choked on a rather large bacon rasher, had ultimately lost. Teyla laughed along, but her thoughts were still stuck on the man sitting next to her.

"So, what are you gonna do today?" Ronon asked Sheppard, his eating pace significantly slowed now that he had won. Even Rodney was taking his meal at a more cautious rate having learned his lesson.

"I fully intend to do absolutely nothing," John answered. He smirked at Rodney across the table, and then held up the tablet PC. Once again he had trumped McKay's score by a landslide. The astrophysicist, completely unprepared for taking two defeats in the space of five minutes just huffed irritably. He would get his revenge on both men later. "Though apparently, that isn't going to happen."

Teyla followed John's line of sight to see Major Lorne making a bee-line towards them. He paused at the edge of their table, his expression apologetic. "Sorry sir, but there's a problem in one of the labs…"

"It's not the laptop thief again is it?" Rodney interrupted. John rolled his eyes while the others looked confused. McKay had enlisted his help the night before in tracking down the elusive thief that had stolen his laptop that was somehow preciously different from every other on Atlantis. It turned out that a new recruit had borrowed it by accident, though Rodney was nowhere near forgiving the error.

Lorne shook his head to cover his own confused expression, and then continued. "Dr. Fredericks wants to talk to his marine details' superior following some mishap – apparently, being acting military commander isn't good enough."

"I doubt being _actual_ military commander will do much good either," John shrugged as he stood up. He had dealt with the uptight scientist before on multiple occasions. It was never a fun experience. He gave one of his small waves as he followed Lorne out of the mess hall, leaving the others behind.

Rodney watched them go, and then glanced at his watch. Immediately he hopped to his feet, stealing John's abandoned computer, and moved to leave as well. At Teyla's curious look, he felt he maybe should explain himself and so paused in his escape. "Carson comes back from M34-J82 today. He's gating in at 8.30 and I said I'd meet him. Before I go and do other far more important things of course."

He covered before he hurried off. She always found it strange how Rodney would rarely admit that he actually cared about other people. Carson was his best friend, she knew, but still he had to cover the fact that he was excited to see him for some reason. Teyla shared a look with Ronon as they finished their breakfasts.

Between computer card games and weird social behaviour she doubted she would ever fully understand the Earth people.

* * *

><p><strong>(Present) 10.40am – Central TowerLevel 25 – Section Delta**

_Okay…ow._

So it wasn't the most eloquent just-woken-up thought he had ever had, but it pretty much summed up the way he felt. Major Evan Lorne found himself sprawled on his stomach, arms splayed as if at least some conscious part of him had decided to break his fall. Gingerly, he rolled himself onto his back, trying to piece his pre-passing out thought processes back together.

There had been an explosion, he knew that much. A lab up on the 29th level of the delta section of the central tower had suffered some major malfunction that in true Pegasus-style ended with something going boom. He had been on his way to the hot zone, yelling instructions over his radio when all of a sudden the world tilted sideways. Lorne briefly berated himself – he'd only been acting military commander for a few hours, and he'd ended up fainting in the middle of an emergency.

But this wasn't the time. There were far bigger things than why he had ended up on the corridor floor; say for instance – a massive explosion. He checked his watched as he climbed to his feet, again rebuking himself when the corridor spun a little, worried by the fact that it had been a whole ten minutes since the emergency call had been made.

"This is Major Lorne, I need a sit-rep from the hot zone."

Static. Okay, he knew he'd missed the last ten minutes, but that was no reason to give him the silent treatment. He tried again, injecting as much authority into his voice as he could – he was the man in charge after all. Still, there was only silence in his earwig. He tapped the radio twice experimentally, a reassuring click confirming that the device was indeed working. It was just that nobody was answering. Something was definitely not right.

Well-honed senses were then on alert. He was only four floors down from the hot zone and yet there was no noise. There should be shouts and questions, the calls co-ordinating the response over the radios and the thrum of machinery as necessary. And yet there was just an eerie silence. The complete lack of activity was making Lorne feel very alone. He unclipped the top of the sidearm holster on his thigh.

"This is Major Lorne, does anyone read?"

He tried again as he continued towards the transporter at the end of the corridor. There were hundreds of personnel on Atlantis then – how could _none_ of them be responding? The lights were still on and the transporter door opened at his command, so they still had power. That was usually the first thing to go if they were under attack. Yes, he was thinking worst case scenario, but what else could explain the complete silence?

He selected a dot on the transporter screen that would take him up to the hot zone floor. With a flash of white light that he barely noticed anymore, he was teleported higher into the central tower. The doors opened with their usual whoosh, and suddenly Lorne found himself in the middle of the most ordered chaos he had ever seen.

Compared to the emptiness of his previous location, the corridor he now stepped into was practically teeming with activity. People he recognised, along with new recruits that he didn't, streamed around him, not one pair of eyes meeting his. It was disconcerting to say the least. Considering he was literally around the corner from the hot zone, the silence in which everyone moved was beyond odd. "Hey! What's going on?"

Evan Lorne had never been so completely blanked in his life – and he'd been the arty-type in high school. If he thought there was something wrong before, he knew that something very Pegasus-Galaxy-weird was happening now. He pushed through the crowd that managed to always get in his way until he found a very familiar face. "Henson!"

The young lieutenant who had been on his gate-team for nearly four years ignored him. Lorne was getting a little bit irritated by the lack of co-operation. He grabbed Henson by the arm, effectively halting his progress, and spun the young man round to face him. "Henson! What the hell is happening?"

Lieutenant Henson blinked very slowly, though his eyes remained unfocused. He removed himself from Lorne's grip and studied his superior officer. Lorne watched as recognition slowly dawned on the young man's face, though it turned out _not_ to be the recognition he wanted. "You are not of the Collective."

"Excuse me?"

All around them, all activity ceased. Everyone went from completely ignoring Lorne, to now staring intently at him. He almost missed being practically invisible. It was weird how they all moved as one, and yet at the same time acted independently. Their movements were almost robotic in nature, while their blank expressions reminded him of mind-controlled zombies. Seriously – what the hell was going on?

"You are of Military Class; rank Major. You have been assessed as a threat to The Collective," Lieutenant Henson said in monotone. Lorne really didn't like where this was going, his eyes already searching for an exit as his hand went for his sidearm. "The Voice decrees that you are to be terminated."

_Oh, so not good._

Henson lifted the P90 clipped to his vest as Lorne drew his sidearm.

* * *

><p><strong>(Present) 10.50am – Beta TowerLaboratory Sierra74-F **

Life in the Pegasus Galaxy is pretty tough for brilliant scientists; especially with both sleep and coffee being rare commodities. It generally led to said brilliant scientists catching some shut-eye pretty much wherever they stood, or preferably, sat. As such, Rodney McKay – self-proclaimed as the most brilliant of said brilliant scientists, had often found himself waking up in the oddest of places. Hence why he wasn't greatly surprised to find himself bent at a perfect right angle at the waist across a desk; his feet on the floor while his upper body squished his laptop flat.

It was right up there in the Top-10 weirdest positions, but it definitely wasn't number one. That was reserved for an especially scarring wake-up he'd prefer to forget.

With a disorientated grunt he pushed himself up and back, promptly falling into a chair he had forgotten was there. He was immensely grateful for it – the floor was probably even less comfy than the desk. He blinked around him, trying to remember whatever was going on before his cat-nap. He was in a lab, but not his one. He briefly remembered his actual lab being commandeered for some test or other that was completely beneath his intellect, leading him to search out another sanctuary. Apparently, this shoebox of a lab had sufficed enough at the time.

He leaned forward automatically to grab at his omnipresent coffee mug, only to find it absent. Confused, he leaned forward in his chair in a half-hearted search for the precious caffeine. He was very disappointed to find it on the floor, the contents spilled in an impressive puddle – he'd barely had a sip before…

Before what? When had he dropped…?

The explosion.

"Sheppard." Rodney muttered, his eyes widening as the shards of memory finally slotted back into place. Lorne had called over the radio that there had been an explosion in Lab Delta29-B – a lab that only twenty minutes before had required an ATA user to act as a human light switch. Rodney had laughed as he eavesdropped on the conversation where John had been bullied into helping out – it was his day-off after all, it wasn't like he was doing anything. And now…

"Please don't be dead," Rodney whispered. He'd lost too many best friends; he didn't think he could handle another. In fact, he was pretty sure the only reason he was managing was because he had had John to help him through. Steeling himself with a deep breath, Rodney tapped his earwig. "This is McKay – any word on the explosion?"

He was expecting an impatient, automatic answer from whoever had been put in charge of fencing panic calls. What he got instead was nothing. Just the dreadfully empty hiss of static. "Hello? Does anyone read?"

"_Oh thank God, Rodney! I've been trying to get a hold of anyone for the last five minutes!"_

"Carson?" Rodney answered, slightly confused. Shouldn't Beckett be at the lab helping the survivors…_if there are any?_ He shook his head against his own thought, instantly regretting it when a headache made itself known. "What the hell is going on?"

"_I have no idea,"_ Beckett replied, sounding just as bewildered as Rodney felt. _"I got the call about the explosion – then suddenly I woke up on the infirmary floor with Captain Burton hovering over me declaring me a low threat or something. He tried to arrest me, broken arm and all. I had to sedate the poor lad for fear he'd do himself more harm."_

Now Rodney was really confused. "Wait…'low threat'?"

"_I don't have a bloody clue. He said I was a 'low threat' to some collective or other because I was a civilian. He was on some pretty strong pain meds."_

"Have you been able to contact anyone else?" Rodney asked, deciding that the high marine was irrelevant to their current situation. He was more concerned with what was _actually_ happening, not what some drug-induced grunt _thought_ was happening.

"_I heard Major Lorne on the radio about five minutes ago, but I was a wee bit busy wrestling my one-armed patient. I tried to call him back but I got not answer."_

Worrying, to say the least. It didn't seem that anyone was at all concerned about the explosion. And for some reason no one was using the radios either, well, at least not for long anyway. Something was definitely going on, and it was nothing good.

"Okay, it doesn't sound like help is getting to the lab where the explosion occurred, so it makes sense that we should head there. There are probably survivors that are going to require your voodoo" _like Sheppard_, he thought, but feared voicing his concern would make it valid. "We'll meet outside the transporter on level 29 in delta section. It should only take about five minutes."

There was a pause over the line, and Rodney knew that the doctor had nodded, obviously forgetting that he couldn't actually be seen. _"Right. I'll see you there."_

McKay signed off the radio call; made a last ditch attempt to hail anyone else, then collected up the tablet PC he had stolen from John that breakfast. He had practically broken his laptop in half when he had collapsed on it, and besides, the tablet was more portable. At the door he took a deep breath before waving his hand over the control. He honestly had no idea what he would be stepping in to.

Thankfully, the corridor beyond was completely clear. That wasn't unusual – the beta tower was a far lower traffic area than the central tower; the quiet was probably why he had selected it for his temporary lab. Even if it was miles away from key places; say the mess hall and its vital coffee machine.

Soon, though, the quiet became very eerie. Yes, the beta tower was usually pretty scarce of people, but it was never _this_ empty. Rodney found himself clutching the PC a little tighter, as if that would actually help him. His pace slowed to an extremely cautious and tense walk, his eyes darting nervously into every dark corner. He had no idea what he was afraid of, but he found himself jumping at shadows regardless.

That was probably why he jumped sky high when he actually did meet another person.

"Zelenka! Thank god!" Rodney gasped. He then quickly hid his previous fear and present relief under a well-rehearsed disguise of arrogant indignance. "You scared the crap out of me! What do you think you're doing prowling through the corridors like some kind of ninja assassin? You realise there are other people around who don't really appreciate being jumped out at. Seriously, if you're going to lurk, at least wear a bell so the rest of us know you're coming!"

Zelenka stood completely still throughout the whole spiel. He fixed McKay with an unfocused stare. When Rodney finally paused for breath and looked at the scientist properly, he realised there was something distinctly odd about him. The way he just stood there was unnerving Rodney to no end. But it was worse when he spoke.

"You are not of The Collective."

"Collective…?" Rodney remembered what Beckett had said about the high marine. Captain Burton had then attacked Carson following that statement. Rodney looked in Zelenka's eyes, but the Czech scientist wasn't looking back. Something _really_ weird was going on. "Oh no…"

"You are of Scientist class. Your threat level has been assessed as low. The Voice decrees that you are to be contained."

McKay caught the briefest glance of the wraith stunner in Zelenka's hand, and then he turned tail and ran. At that moment, Rodney was incredibly grateful for the last five years he had spent on Sheppard's team – it had taught him to run _really_ fast. The first shot hit the wall behind where his head had been, but he was already half-way down the hallway, doing his best to not panic.

The funny thing was, he was Rodney McKay, and he had a tendency to panic.

Flashes of blue sputtered around him as he began a freaked monologue under his breath. The stunner, though technically harmless to him, was still made of kinetic energy that blasted the corridor around him. Still talking, his main defence mechanism, McKay kept running. He took every turn he could see – already completely lost, but that didn't matter as long as it lost his pursuer too.

Eventually, the stunner blasts got fewer and further away and McKay allowed himself a moment of triumph when a transporter came into view. He skidded to a stop in front of the door and was just about to wave his hand over the control when a tell-tale flash of white shone round the frame. The doors opened to reveal two well-armed marines.

"Are you homicidal zombies as well?"

The twin stunner blasts to the chest answered that question.

* * *

><p><strong>Woot! I finally finished this chapter. I started and abandoned it at least twelve times lol. I hope it isn't too confusing, I'm going to start actually answering the 'what the hell?' questions that every character has so far asked next chapter…<strong>

**Please let me know what you think!**


	2. Escape and Evade

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

Wow! Super-duper thanks to sherry57, firefighter22, highonscifi, JoeyLuv, BMick, shirik, Questfan and sheppardlover928 for reviewing! My muse appreciates you all! Also to everyone else who alerted, favourited and/or simply read the previous chapter – you are all wonderful as well!

Also; 'Present' is now a blanket-term that covers anything post-explosion. The scenes are technically out of order so you'll probably need to pay special attention to the times in the subtitles – but from the reviews I'm guessing you guys are following the time-shifts okay so I'm going to stop nannying now.

Now to ignore my ramblings and get back to the actual story!

* * *

><p><strong>Chapter Two -:- Escape and Evade<strong>

**(Past) 08.30am – Central Tower/Stargate Operations**

McKay practically ran the last length of corridor, though he skipped to a casual stroll the moment he approached the gate room. He tugged at his uniform and slowed his breathing all to hide the fact that he had in fact been uncharacteristically eager for a social event. He hadn't seen his best friend for nearly two months, the ever-the-good-Samaritan doctor having been giving aid to a planet ravaged by the Hoffan virus. Beckett was only going to be home for a few days, and he'd probably spend them working, so Rodney was going to very subtly spend as much time with him as he could.

He didn't want to appear desperate or anything.

He entered into the vast gate room with a smile he couldn't remove glued to his face. For all his pretences to the contrary, he couldn't help but feel excited. He probably gave himself away when he actually acknowledged another human being's existence with a jaunty wave. The gate tech he gestured to gave him an almost frightened look and quickened his pace, but Rodney didn't care. He checked his watch as he came to a stop at the bottom of the steps. He was dead on time.

The gate remained stubbornly inactive in front of him. Rodney made a thoughtful hurumph, and checked his watch again. Maybe Carson's was just running a little slower than his, therefore making the doctor not technically late. It was only thirty seconds after all…thirty-two…thirty-three…

"Scheduled Off-world Activation!"

"Well that's not true," Rodney muttered irritably as the chevrons around the gate glowed to live with a low mechanical whir. "He's thirty-seven seconds late."

He waited as close to patiently as he ever got as the vertical blue pool of the Stargate materialised with a majestic whoosh that Rodney barely took any notice of. He'd seen it enough times for the once amazing sight to have dulled to an everyday occurrence. Eventually, the wormhole locked, and Rodney tapped his foot waiting for Carson to appear.

Instead, a large black duffle bag flew through. Seconds later it was joined by another. Nearly a whole minute after that, Beckett struggled through the gate backwards, dragging a huge and rather heavy looking yellow box. Rodney watched him struggle for a moment as punishment for the man's tardiness, and then came forward to help. "About time you showed up."

Carson threw Rodney a tired grin. "You missed me then?"

"You? No, of course I didn't miss _you_," Rodney put as much arrogant indignance in his voice as he could. After nearly four decades of practice, he pulled it off pretty well. "I simply don't appreciate being asked to be at a certain place at a certain time to help out and then being made to _wait._ It's just not the way we do things in civilised society."

Beckett could read him like a book and didn't take any of the rant to heart. He just continued to smile tiredly as he grabbed up one of the casually tossed duffle bags. Rodney picked up the other and between them they dragged the box out of the gate room. "Anything interesting happen while I was away?"

McKay shrugged, quite a feat considering both his arms were being stretched by luggage. "Not really. Sheppard's managed to lead us on eight missions with the worst injury received being a rather nasty splinter – don't worry, I had Jennifer look at it. She says I'm fine, and when she says it, I actually believe her." Carson's smile broadened at the love-sick puppy look on his friend's face. "Woolsey has imposed at least twenty new rules that no one has bothered to obey; Torren can now successfully sit up on his own and the _Apollo_ deposited a whole bunch of new recruits – one of whom stole my laptop yesterday."

Beckett didn't immediately reply as the pair of them struggled down a poorly designed spiral staircase. "So you and Jennifer are serious now?"

"Ever since we spent some quality time avoiding a catastrophic disaster in Nevada things have been really great," Rodney was grinning like a kid. Carson remembered when he had first met the astrophysicist more than five years prior; he never would have pegged him as the relationship type. "She's amazing Carson…and she likes me. I mean, come on! She actually likes me!"

"Unbelievable," Carson muttered good-naturedly. It took Rodney a moment to catch the bantered insult, and then they were both laughing. McKay really had missed his best friend.

"Hey! Need a hand?" a voice called from behind them. Rodney turned slightly to see Sheppard jogging towards them, not even slightly out of breath while the pair of them were panting like dogs. He took the duffle bag from Beckett with ease and the doctor then took the yellow box by himself. "Where you heading?"

"The infirmary," Carson answered, grateful for the help.

"Brilliant, the complete opposite direction of where I need to go," Sheppard grinned, matching pace with the worn down men. At Rodney's look he elaborated. "Woolsey wants to see me about something."

"I thought it was your day-off."

"I told him that, but apparently paperwork waits for no vacation time." They turned a corner and the infirmary doors finally came into view. Rodney sighed heavily in relief and Sheppard threw him a sideways smirk at his lack of fitness. He remembered only months before when Michael had stormed Atlantis, shutting down power and the much-relied-on transporters; forcing Rodney to use the stairs. John had been barely taxed while the scientist had been practically floored by the exertion. The moment they entered the infirmary they dropped their loads, Rodney dramatically throwing himself on an unused gurney for a much needed nap. John prodded him. "Bythe way, I passed McKinley on the way up…"

"Who?" Rodney asked, his voice muffled by the pillow he had face-planted.

John sighed then proffered the computer he had tucked under his arm. "The laptop thief. She said she was sorry about five hundred times and that she didn't change any of the settings too drastically. At least that's what I think she said – she was speaking at the speed of light at the time."

Rodney gave a grunt of acknowledgment and blindly reached for the computer. Safely back in his possession he held it almost like a treasured teddy, the look completed by the napping. John rolled his eyes, said his goodbyes and left the infirmary.

Carson came and perched on the edge of the gurney next to Rodney, rolling his shoulders experimentally. His muscles burned from the strain of lugging the heavy equipment, but it was all necessary for him to continue his research. The guilt from having helped Michael create the Hoffan drug drove him to work beyond human endurance. He would never rest easy until he had managed to right that terrible wrong. Unlike Rodney, who was looking very comfortable.

He gave the astrophysicist a poke in the ribs and was rewarded with an irritated mumble. After a minute or so of continual prodding, Rodney eventually pushed himself upright, swatting Beckett's hand in annoyance. "Don't you have work to do?"

McKay grumbled something unintelligible.

"That was a 'yes', wasn't it?" Carson smiled. He himself had a ridiculous amount of work to do, that was honestly going to be easier to complete if Rodney was otherwise occupied.

"My lab may currently be being used for some 'social science' experiment that has no right to be called a 'science', but yes, I do have other important things I should be doing," McKay sighed, rubbing his eyes. Now begrudgingly awake he remembered his stupidly long to-do-list. "There's some lab down in delta that the laptop thief discovered yesterday – I need to delegate the cataloguing to some overpaid underlings. I also need to find a new lab, run diagnostics on some power fluctuations Zelenka's been moaning about _and_ re-re-write a mission report Woolsey found unsatisfactory."

Carson raised his eyebrows, patting Rodney sympathetically on the shoulder. He then stood aside and gestured at the door. "Don't let me keep you."

With another sigh, McKay hopped off his gurney and onto his feet. He hated that he had so little time with his best friend; even when they were on the same planet they hardly got to hang out. "Fine. But we'll meet up again later. I'll come back and make sure you stop for lunch."

"I'm sure you'll remember." Carson said non-committedly. He'd been stood-up by Rodney's forgetfulness enough times.

"I never forget lunch!" Rodney called over his shoulder as he headed out the door. "Unless of course we're being invaded, sieged or otherwise attacked."

"Here's hoping for a quiet day."

* * *

><p><strong>(Present) 10.55am – Central TowerInfirmary **

"_We'll meet outside the transporter on level 29 in delta section. It should only take about five minutes."_

Beckett nodded in agreement to Rodney's plan, then abruptly realised he couldn't actually be seen. "Right. I'll see you there."

With that decided he cobbled together an expansive emergency med kit. He knew Dr. Keller had been pretty close to the explosion when it happened and was the first responder, but Beckett determined that it was better to be safe than sorry. Without anyone answering the radio it was impossible to tell what was going on and who needed his help, so it made sense to be ready for anything.

By the time he had collected together the additional supplies the five minutes Rodney had allowed were practically up. He tapped his radio to let the scientist know he was running late. "Rodney? It's Carson, I'm just leaving now."

He didn't receive a reply. "Rodney?"

_Now that's not good _Carson thought to himself, his anxiety doubling. He glanced at the infirmary door as he hitched the kit over his shoulders. Something was going on out there; something really bad. Something that was silencing everyone on the other end of the radio. The fear of the unknown enemy made Carson reluctant to leave the relative safety of the infirmary; but he was a doctor, and there were people out there in need of his help. He squashed the fear down as best as he could, took a deep breath, and stepped into the corridor beyond.

Thankfully, he found the it empty. That was unusual though, considering the infirmary's proximity to Stargate operations, the nerve centre of Atlantis. After only a few seconds, Carson was incredibly creeped out. Where the bloody hell was everybody?

"Rodney?" he tried the radio again, flinching at the volume of his voice in the deserted space. Still he received no reply. Carson felt every muscle in his body tense as he forced himself to keep going. The strange emptiness of the usually busy area reminded him of some terrible horror movie Rodney had made him watch. There had been zombies in that movie. Carson _hated_ zombies.

He made his way down a staircase and along several more corridors without meeting another soul. He was only a few turns away from the transporter. He picked up the pace at the promise of an end to the eeriness, taking a corner at a near run; and then froze.

He found himself at the business end of a standard issue sidearm.

"I don't know who you are and I don't really care. I will shoot you if you try any of that robot-cop crap on me." The owner of the gun declared with far more confidence than her shaking hands betrayed. She looked a little traumatised, a bruise forming on her cheek and dribble of blood on her lip.

Judging from her civilian uniform, Beckett concluded that the gun wasn't hers, but he didn't doubt that she could use it. He raised his hands as non-threateningly as possible. "Easy lass, I'm not going to hurt you."

She studied him intently for a moment, noting his non-robotic speech. She relaxed a little, but still didn't lower the gun. "Are you…are you…normal?"

"Aye, lass, or so I've been led to believe," Carson used his best bedside manner voice, smiling gently and reassuringly. It had the desired effect as she carefully lowered the weapon.

"Good, cause I didn't really want to shoot you," her dark eyes darted around the corridor that was still vacant apart from them, shifting nervously from one foot to the other. "I've only been here two days and I don't particularly want to gain a reputation as some trigger-happy psychopath. I hate being new, don't you? Particularly when you're in another _galaxy_ and you don't know anybody and then you wake up to your bunkmate from the _Apollo _suddenly attacking you like some kind of B-movie zombie. I'm Miranda by the way, Miranda McKinley."

Carson blinked, struggling to keep up with the woman. "Dr. Beckett."

"Nice to meet you,Dr. Beckett, especially as you're not trying to attack me." McKinley replied, now practically dancing on the spot. He wondered if it was from nervousness or if she was naturally that restless. "We should keep moving; they catch up to you if you stay still for too long. Are you going anywhere in particular?"

Beckett made a show of his med kit. "I'm a doctor, lass. I was heading towards the accident to help the survivors. You're welcome to join me."

"Sure, that's tons better than being on my own anyhow. Safety in numbers and all that." McKinley fell into step beside him as he continued down the corridor. She lifted the gun back into a ready position, scoping it from side to side.

Within minutes they found themselves at the transporter and he waved his hand over the controls to open the doors. Carson was a little nervous about trapping himself inside such an enclosed space with strange, armed woman, but as she had said – it was better than being alone.

They stepped inside, Carson selected the appropriate dot, and suddenly they were bathed in white light as they were teleported down the building. The doors reopened with a whoosh and they stepped into a hallway practically identical to the one they had just left behind.

They barely made it down two corridors before they found themselves in a warzone. Bullets and stunner blasts ricocheted around them, the sound deafening compared to the previous silence. Beckett instinctively grabbed hold of McKinley and pulled her down, shielding her with his own body. He chanced a glance up and saw Lorne taking cover behind a pillar further up the corridor, firing sporadic shots from his hiding place. "Major!"

Lorne turned at his title and saw the pair of them cowering in the small amount of cover they had found for themselves. Carson saw the debate play out across the soldier's features as to whether or not they were enemy combatants as well. He seemed to decide they weren't though as he lay down a series of shots to pin down the enemy then ran from his cover, closing the distance between them.

"Can't go this way, doc," Lorne quipped as he hooked a hand under McKinley's arm and hauled her to her feet.

Bullets continued to sing around them as the Major shoved them back the way they had come. He stifled a yell as a bullet found its target, but continued their retreat without pausing. He fired off a shot or two over his shoulder until his gun clicked empty. Eventually they made it back to the transporter. Lorne jabbed a random dot on the map and they were whisked away to the safety of the beta tower.

Once they stumbled out of the transporter and into another corridor, Lorne turned on Beckett. "Now please tell me you know what the hell is going on."

* * *

><p><strong>(Present) 11.10am – Sigma TowerLevel 4 – Section Zulu **

John looked down the barrel of the gun currently pointed at his head. He'd been threatened enough times that the actual weapon didn't scare him as much as it probably should; it was the person holding it that frightened the crap out of him. Teyla was staring at him with eyes far colder than he had ever seen them, her grip sure on the weapon poised to kill him. However, she hadn't.

"The Voice decrees that he is to be terminated." Keller repeated, also noting the delay.

There was the slightest of tremors to the hand that held the gun; John only noticed it because it was mere inches from his face. His gaze flickered from the gun to her eyes as he tried to figure out if it was really Teyla in there. He remembered his own experience with Thalen; how he had been totally aware of his actions and yet completely unable to control them. Was she now fighting as he had fought?

The most distinct memory John had from his experience was the guilt from getting Ronon shot and hurting the others. He didn't think he would've been able to live with himself if he had killed one of them. As Teyla fought whatever forced her finger to the trigger, he searched for a way out. He couldn't let her live with the guilt of killing him.

"As the Voice demands…so shall it be."

_This is gonna hurt._

John threw all his weight to the left milliseconds before the bullet left the chamber. The explosive sound practically deafened his right ear from its proximity, but he had succeeded in avoiding the shot. The soldiers holding him had been taken completely off guard – the one on his left was thrown off-balance while the one on his right had been dragged into the bullets path. The force of the hit to the shoulder at close range threw the soldier flying backwards to the ground.

Sheppard was up and moving, adrenaline temporarily masking the pain of his injuries, while the people around him struggled to process what had happened. Maybe whatever was controlling them couldn't make snap decisions, meaning that Teyla and the others lost their reflexes and spontaneity. Whatever the reason for their slowness, John didn't care, he was just grateful. It was the only way he'd ever beat Teyla in a fight.

He easily disarmed her with a textbook move that he never would have gotten away with if she were herself. It was then that they began to react. The off-balanced soldier made a grab for him as Teyla threw a left hook at his face. With a pang of guilt he backhanded her across the cheek with the butt of the weapon as he elbowed the soldier in the nose. With them down, he only had to deal with the hallway full of people.

John saw Keller draw a Wraith stunner and aim it in his vague direction; she never had been very skilled with weapons. He darted forward, simultaneously switching the 9mm to his left hand, freeing up his right to snatch the stunner from her grasp. All around him the others were readying weapons ranging from stunners to P90s, but still their movements were stilted and slow. If he were 100% he probably could have disarmed most of them singlehandedly, but as it stood he decided it was best to avoid the fight.

Stunning a few civilians that were in his way, John pelted down the corridor towards where he hoped a transporter was. He wasn't greatly familiar with this section of the city, even though he claimed to know Atlantis like the back of his hand. Honestly they didn't often have use for the additional cells, instead only really using the one a few levels up for Todd, their regular guest.

With the first turn of good fortune of that day, or at least what he could remember of it, John found himself at a transporter door. Behind him he could hear the sounds of pursuit as his hunters cycled their weapons, the wasted ammunition chipping the walls around him. He threw himself inside the closet-like space and automatically poked at the screen.

When the doors opened again he stumbled out into the familiar corridors of the gamma tower and the crew sleeping quarters. He left the transporter and half-jogged down a few halls just in case one of his pursuers had seen which part of the map he had selected. By the time he came to a stop his breath was coming out in ragged gasps, his right arm pressed tightly against his aching ribs. His head was swimming, whatever he had had for breakfast threatening to make a reappearance. Apparently running for one's life wasn't a good thing to do with a concussion and cracked ribs. Now that the brief adrenaline high had left him he felt the pain ten-fold.

He allowed himself a few minutes to just stand there and recover. Eventually he managed to slow his breathing enough for the burning in his chest to subside a little. The world slowly stopped spinning and his breakfast stayed put, allowing him to try and figure what the hell had just happened.

His memory from before waking up in a decimated lab remained stubbornly blank. He couldn't remember that morning or even the day before – he didn't even know what day of the week it was. The memory loss worried him a lot; but he figured mind-controlled personnel and explosions were slightly more important at that moment in time. The tiny pieces of information he did have didn't fit together anyway, so John decided to prioritise. He wasn't far from his quarters; he'd patch himself up, and then he'd figure out what to do next.

He was still holding the confiscated stunner and sidearm as he began the arduous journey to the other side of the tower and up the stairs. He tried to remain alert as he had been trained, but he couldn't have been that aware as he finally picked up on a distant noise. He was going to blame the fact he was practically half-deaf. As he climbed the stairs the noise became clearer and closer.

Something was crying. Well, wailing would be a better description. John almost kicked himself when he realised who it was.

"Torren."

* * *

><p><strong>(Past?) 10.30am – Central TowerStargate Operations **

The explosion rattled the glass windows of Woolsey's office. The floor shook, light fittings swayed and the photo of his beloved dog fell to the ground with a crash. Woolsey gripped the edges of his desk in fear as well as support until the tremors stopped.

Whatever he had been working on before was instantly forgotten as he leapt to his feet. He could see the gate technicians immediately jumping to action in the control room as they tried to pinpoint the explosion's origin and assess the damage. Woolsey was marching across the adjoining bridge from his office as the first radio calls came in. "What just happened?" he demanded of Amelia as soon as he was in earshot.

"We're not sure, sir," she replied, a concerned look on her face although she was perfectly calm as she navigated the control room's computer systems. She always had been good under pressure; and she was a pretty good kick-boxer as well. "We're getting reports of an explosion in delta section."

"Patch me in," Woolsey ordered, and immediately his earwig was full of radio chatter. He decided to try and bring some order to the chaos. "This is Woolsey, can someone please tell what has happened."

"_This is Keller, I'm at the scene. It's lab delta29-B that's exploded. I've been told that there were people inside, but I can't get to them because of the rubble. I need combat engineers down here ASAP."_

"_Beckett here, Jennifer love, do you need me to come down?"_

"_No, I need you to prep the OR, if there are any survivors they're going to be in pretty bad shape."_

"_Understood. Out."_

Woolsey shared a look with Amelia. Things didn't sound good. He briefly wondered how many good people he had just lost, before he was able to bury the thought. There was still a chance, and they would do everything physically possible to help. "Major Lorne, can you co-ordinate the engineers? We also need to know if this tower is still structurally sound so that we can organise an evacuation if necessary."

"_This is McKay. I've shut down all primary power to that area but it's taking longer to isolate secondary systems so watch out for live electrics."_

"_Thanks doc," _Lorne replied. _"Greggs has reported that the tower is still safe, there's no need for an evacuation. The rest of the engineers are on their way Keller, hold tight."_

Woolsey let out a breath he hadn't realised he was holding. He didn't want to think about the disaster they could have been dealing with if they had needed to evacuate. This way, at least, they could focus on rescuing the survivors. "Do we know who was in the lab and what they were doing?"

It was McKay who answered. It was his department after all. _"I assigned the lab to Parsons and Volkov for investigation and cataloguing."_ There was a pause over the line. _"They called for an ATA user…I think…I think Sheppard's in there too."_

"Understood," Woolsey said, mainly because he wasn't entirely sure what else he _could_ say. That was three people, and one of them was his military commander. But he had to stay focused, calm and in control; he was the leader of this expedition and he had proven before that he could handle the pressure. "Major Lorne, what is your status?"

"_The combat engineers are at the hot zone. I'm currently en-route, ETA fi…"_

"I'm sorry Major, didn't catch that last part." Woolsey tapped at his earwig, and then glanced at Amelia when he didn't get a reply. She shrugged, indicating that the equipment was fine. "Major?"

The gate technician next to Amelia promptly slumped across his console. She immediately leaned over to check on him. "Harvey? Harvey can you hear me?"

"_Hello? This is Keller. I can't get through to Beckett. Rodney is there a problem with the radios?"_

Again, there was no reply from either man. Now what was going on? "Major Lorne, Dr. Beckett, Dr. McKay, report." Woolsey instructed with as much authority as his voice could project. Still, there was no reply. "Dr. Keller, we seem to be having difficulty reaching some people. Focus on helping the engineers while we sort out the problem. Amelia, call Zelenka and ask him to run diagnostics on the communications system."

"Yes sir," Amelia begrudgingly left Harvey in order to make the call. The poor man had only been there as long as her so she guessed they were both relatively green to the expedition, but she didn't understand why he had fainted. "Zelenka says there is no problem, sir."

"Strange. Keep trying to contact Major Lorne and the others. Chet," Woolsey called Chuck, who under the circumstances didn't feel the need to correct him. "Help Harvey…"

Suddenly, Woolsey's world became very dark.

The Voice found itself standing in the middle of a strange room it hadn't seen for a very long time. It recognised the elegant décor and crystalline technology to be that of the Ancestors; however it was confused to see perplexing silver boxes attached to nearly every console. Much time must have passed since the last time The Collective had been free.

Inside the room were Ancestor-shaped beings, although their bizarre dress made it apparent that they were not in fact, the Ancestors. Unless of course they had experience a radical change in fashion trends. It wouldn't have been that unlikely, had it not been that the Ancestors were extremely set in their ways. The Voice turned to one such creature, a female with fair hair and skin. She met its gaze, and the Voice found a kindred. She had taken the designation of her host; she would be called 'Amelia'.

"What does the Voice demand?" she asked, her voice perfectly pitched in a monotone. Other members of its kin were also looking to it for guidance. They had woken up in a new world; a world stolen from them before – but this time they would seize it and never relinquish their control.

"Begin memory downloads; update current history archive." The Voice commanded. It wanted to know what it now controlled, the better to fully appreciate what they had achieved. The Voice made its host turn and walk over to an odd shaped perch at the edge of the room. It looked down at the cavernous room below, and the cursed ring it housed. Last time they had lost everything because of that ring. "Shut down the Ring of the Ancestors. There will be no outsiders."

'Amelia' learned how to operate the console from her host and easily found the gate-shield control. The blue film instantly formed across the ring. "Partial memory download complete 12%. Commence broadcast?"

The Voice nodded from its perch; its host's eyelids flickering as it received the data package. It had been over 10,000 years since The Collective had last been free. The Ancestors that had imprisoned them had long since been eradicated, leaving their great city to these mere humans. The humans were divided into classes; Military, Scientist and Civilian, and were helpfully colour-coded as well. The Voice ordered for The Collective to assume the role of its host, his order heard by all throughout the city.

Atlantis now belonged to The Collective.

"What the hell?"

'Amelia' and the one designated as 'Chuck' looked curiously at the human between them. The man wore the same uniform as their hosts and appeared no different from them. And yet he had not assimilated. 'Amelia' looked over at The Voice, communicating the oddity. "He is not of The Collective."

"The what? Amelia, what are you talking about? What happened?"

The Voice grew irritated; a memory from their last Awakening coming to mind. The Ancestors had managed to immunise themselves from their influence – had they managed to do the same to the humans? This complicated matters; their control was not absolute until they were the only free beings in the city. The Voice decided that the uninfected one would be useful for research later. "Contain him."

"What?"

"The Voice decrees that you are to be contained. Surrender willingly and you will not be harmed."

The human's eyes were impossibly wide as he tried to comprehend what was happening. The Voice found his confusion most amusing. He tried to escape, however it appeared that 'Amelia' had also learned a degree of skill in hand to hand combat from her host. She knocked him out with ease, and then ordered a member of the military class to take the human down to the holding cell.

"There may be more," The Voice said both verbally and telepathically as it addressed every member of The Collective. "Take arms. Find them, assess them and neutralise them. Begin excavating the Origin. Our second genesis has begun."

* * *

><p><strong>(Present) 11.20am – Sigma TowerHolding Cell Zulu2-C **

McKay woke up to the familiar pins-and-needles-all-over sensation he always got after being stunned. Still disorientated, his eyes not yet open, he half-expected to find himself on yet another hive ship about to be Wraith-chow. He was almost relieved when he actually found himself in a different yet just as familiar cell. He had found himself locked up in their own prison on Atlantis enough times to recognise it purely from the ceiling.

With a groan he pulled himself into a sitting position and took proper stock of his surroundings. He was actually in a different cell from the usual – this one was a larger pen-like space, designed to house more than a single Wraith or a handful of people. This cell could easily hold 30 plus people, and currently contained around twenty. He glanced round at a bunch of familiar faces in varying shades of passed out or petrified, but didn't find anyone he particularly wanted to talk to. Instead he climbed onto his feet and wandered over to where two zombie-marines were standing guard.

"So...mind filling us in on what's going on?" Rodney asked, sarcastically upbeat. Neither guard made a move to reply, not that he was actually expecting them to.

"They won't answer." Rodney glanced down at a green-uniformed person slouched at his feet. Harvey the gate-tech looked utterly defeated, a dark bruise forming over his puffy left eye. "And even if they did, they'd just hit you with some 'collective' bullshit."

Once again, Rodney picked up on the term 'collective'. Apparently that was the word of the day – even the zombies were using it before they stunned you. Maybe that was the name of whatever mind-control was at work here. Or maybe he had fallen asleep watching Star Trek again and this was all just a dream. And incredibly vivid and painful dream. "You got any idea what's happening?"

"Not a clue. I woke up in the control room and everyone was acting weird. Woolsey ordered that I be 'contained' and Amelia knocked me out. Next thing I know I'm in here, and every now and again they bring in someone else," Harvey answered sourly. Obviously he wasn't taking his bad day well.

"Wait, 'woke up'?" Rodney queried, remembering his own rude awakening and Carson mentioning something similar.

"Yeah. Everyone here will tell you the same story. We all passed out, and when we woke up again it was the damn zombie apocalypse."

"Huh," McKay muttered, adding the information to everything else he'd learned. He was still completely in the dark, but he had stopped dismissing intel when a high grunt had proven to have said something relevant. He turned back to the guards, leaning as close as he dared to the invisible force field to try and catch their eye. "Hey! Could you at least tell me who you are? That'd be great. No? How about why then? Come on, you can't ignore me forever; I've been told I'm quite persistent." Rodney paused, half-hoping his interrogation method of 'be as annoying as possible' was having an effect. "Fine. Can you tell me what do you intend to do? Have you got an ultimate goal or anything?"

Finally, one of the guards answered. "We are The Collective. Atlantis belongs to us."

* * *

><p><strong>AN: BTW, really randomly, there is a method to the madness of the location names – in the show they never have to explain where the characters are beyond vague establishing shots, but I needed specific locations to make things easier, so I decided to make some up. The tower names are taken from the Greek alphabet and section titles from the NATO phonetic alphabet. Particular rooms are made up from function/section/level/room. It doesn't really make any difference; I just thought I'd tell you anyway.**

**See you next chap!**


	3. Babies and Breakouts

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

Thanks again go to all my awesome reviewers; I'm glad you're all enjoying the story so far and that you're following the time shifts okay!

On that note, I have now dropped 'present' as 80% of the chapter is set post-explosion. I'll put 'past' on flashback scenes just to make things a little clearer.

Also, sorry for the lateness of this update, I've practically been living at work this week lol. Enjoy!

* * *

><p><strong>Chapter Three -:- Babies and Breakouts<strong>

**11.10am – Beta Tower/Level 78 – Section Charlie **

"Now please tell me you know what the hell is going on?" Lorne asked once he had finished a cursory sweep of their new location. He guided them away from the transporter and into a lab, locking the door behind them. He doubted it would hold if the others caught up to them, but the minimal security was comforting nonetheless. Once safe, he turned back to Carson and the woman. "Well?"

Both of them shrugged, looking just as confused and frustrated as he felt. Lorne had to admit, if only to himself, he was glad he wasn't the only normal one left on Atlantis. Of course, he'd rather he had found a squad of unaffected marines rather than two civilians, but just being able to talk to another human being that wasn't trying to execute him was good enough for now. And, he surmised, if there was even more normal personnel out there it was likely he could find that squad of marines later.

"We don't have a clue, Major," Beckett answered. The doctor caught sight of the fresh bullet wound in his arm that had got nicked while he was helping them escape. He shrugged off his medical kit and gestured at it. "I should probably take a look at that, son."

Lorne nodded and sat himself on a stool while Beckett busied himself with his equipment. He barely reacted when the doctor began cleaning the wound; he'd been shot enough times to be relatively immune to the pain. He also knew from experience that it was only a flesh wound – he'd been lucky under the circumstances. "What do you know?" he asked. It was the woman who answered.

"We know that whatever is going on has something to do with a 'collective' and nope, we don't know what that is," she explained quickly. Lorne noticed then that she was carrying a gun and wondered where she'd got it. "It's turned everyone into robotic zombies that are trying to capture us for some reason. They act like they're communicating telepathically or sub-sonically, or maybe wirelessly." A look of horror crossed her features. "They're not…replicators…are they? You guys destroyed them, right?"

"They're not replicators," Lorne stated certainly. He looked away with a guilty expression. "They bleed when you shoot them."

"Oh my god," Beckett breathed, pausing mid-stitch as he tried to catch the major's expression. "Did you…? What happened, son?"

Lorne closed his eyes for a second; he didn't really want to replay what he had been forced to do, but felt that denial was disrespectful. "I…uh…I…" he paused, swallowed, and decided to start from the beginning, adopting his report giving tone to hide the emotion bubbling beneath the surface.

"I woke up not far from the hot zone and tried to radio for an update. No one replied so I continued towards it. When I stepped out into the corridor it was full of them – there must have been at least thirty, and most of them were soldiers. I didn't figure out that something was wrong until I caught up to my lieutenant. He spoke of the 'collective' as well, and then declared that some 'voice' wanted me executed. I managed to disarm Henson before he got the shot off, but by then I was surrounded."

Lorne stopped again, preparing himself for admitting his mistake. "They opened fire, and I just…reacted. I had Henson's P90 and my sidearm and I fought back. I didn't know who or what they were so I tried to only wound, not kill. But I…I messed up. I was aiming for his shoulder, but I killed him instead. Sargent Walters; he was…he was a good soldier."

From an outsider's perspective it could have been argued that he had had no choice but to fight back. If he hadn't, he would have been killed. It had been an accident that killed Walters; but from Lorne's perspective it was an unforgivable error that he would have to live with. He already planned to be the one to tell the Sargent's next of kin on Earth if they ever got out of this mess.

"I left a lot of the others wounded and bleeding out," Lorne continued, knowing that he was probably responsible for even more death. "They kept me pinned down for a long time as I tried to retreat. I was close to an escape when you two showed up, and you know the rest."

Beckett levelled his gaze with Lorne's, injecting as much sincerity as he could into his voice. "It wasn't your fault, son."

"It was my gun, doc, in my hand," Lorne replied, just as evenly. He would shoulder the guilt he deserved, and no comforting words or empty excuses would ever alleviate the weight of his actions. Beckett caught the determination in his tone and let the matter drop, at least for the moment. Right then they needed to focus on what to do next. "Have you met any others?"

"I spoke to Rodney not long after I woke up," Beckett replied, allowing the subject to change. "I haven't been able to reach him since."

"When I woke up my bunkmate was trying to arrest me," the woman added. "It would make sense that if they managed to capture the other unaffected people they would take them to the holding cells."

Lorne was secretly glad that both of the others had admitted to 'waking up' confirming that he wasn't the only one to pass out. He filed the information away for later; it probably had something to do with why they were unaffected, though as to how that was possible still eluded him. Hopefully they'd find a few scientists that could explain what was happening.

"Alright," Lorne came to a decision, and the other two seemed willing to follow him. "We'll head towards the holding cells and see if we can't pick up some Wraith stunners along the way," he didn't particularly want a repeat of his previous encounter. "We'll try and find the others and break them out if we can.

"Also, we should stay off the radios for now," Lorne added. "If they're smart, and we should assume that they are, they'll have figured out how to monitor communications by now. If they've got control of Stargate operations they'll probably also have access to the city sensors as well. Once we have the others we'll need to head somewhere where the sensors are blind, any ideas?"

"The sensors on the East pier are still damaged," the woman helpfully supplied. Beckett gave her a look to ask how she knew that and she just shrugged. "It was on Dr. McKay's to-do list."

Lorne checked the status of his weapon and was almost glad to find that he was nearly out of ammo. He would gladly change the P90 out for a Wraith stunner as it meant he would no longer be forced to fire upon his own men. They waited as Beckett packed up his med kit and slung it back over his shoulders, and then headed towards the door. "Let's go."

* * *

><p><strong>11.15am – Gamma TowerQuarter Alpha83-T [Teyla's Quarters] **

John doubled his pace as he headed towards Teyla's quarters and her crying child. Once he arrived at the door he was relieved to find it unlocked and it opened as he waved his hand over the control. He closed and locked the door behind him, hoping the security would be enough if any of his pursuers caught up to him. He then went straight over to the baby cage to find Torren shaking the bars in distress.

"Hey, hey little guy, it's okay," he soothed as he scooped Torren up and held him on his non-damaged side. The wailing subsided to sobbing as John gently rubbed his back as Teyla had taught him. Things must be really bad for Teyla to have been forced to abandon Torren. With the baby quieted, John moved on to his next problem. "Okay. Now what am I gonna do?"

Torren looked up at him curiously as if wondering why his new protector had asked _him_ that question. John rolled his eyes at himself "Right…how would you know? Hell, I'm sure you're smarter than me but it's not like you can actually talk yet." Still Torren continued to look at him. He seemed to have mastered the patronising glare already. "Okay, then."

John scanned the room trying to figure out what the hell he was going to do. It was then that he caught his reflection in a mirror, reminding him of his original plan. The entire right side of his face was caked in blood that was worryingly still seeping from the massive gash along his hairline. He looked down at Torren, wondering how the sight hadn't freaked the child out.

"How about you sit here real quiet-like while I go clean myself up, eh?" John muttered as he sat Torren down on Teyla's bed, propping him against the pillows. Torren didn't look too pleased to be put down and recommenced crying. "No, nope, little guy, that's not quiet."

Sheppard looked around to try and find a pacifier or something. His eyes strayed to a half-packed bag of Torren's things. He got up and went over to it, rooking through until he came across a ready-made-up bottle of milk. He shook the bottle in Torren's direction and the toddler stretched out his arms. "You hungry? Of course you're hungry, you love this stuff."

Torren's cries were quickly silenced as he gratefully stole the proffered bottle. He leaned back against the pillows, contented for the time being. John sighed and gave the child's arm a squeeze. "Okay, little guy. You're gonna stay right here for a few minutes, okay? I'm just gonna be in there, no need to cry or anything. 'Kay?"

Obviously, Torren didn't answer, but John found himself talking to him anyway. With problem two currently solved, Sheppard went back to problem one. He disappeared into Teyla's bathroom, pausing for a moment to check that Torren would be okay alone. When the baby made no noise other than slurping, John searched out the first aid box from under the sink.

He was in bad shape. He had known that before, but now that he'd seen himself in the mirror the pain had doubled. His head felt like a menagerie of hyperactive animals had been let loose with power tools, and his chest burned as if he had just run a marathon. John fished out the alcohol wipes from the first aid kit and then looked at his face again, realising they weren't gonna cut it. Instead he found a face cloth and ran it under the tap, using that to scrub away the sticky blood. He'd apologise to Teyla later – if there was a later.

With most of the blood gone he turned back to the wipes and cleaned the wound, hissing as the chemical stung like a bitch. He could feel a lump forming with a purple bruise beneath the gash. He knew the cut would probably need stitches, but he didn't have what he needed to do it himself, so he just left it. The blood flow had mostly stopped anyway.

Then he moved onto his ribs. He stripped off his over shirt, left arm first so as not to stretch his side, then lifted up his t-shirt. The entirety of his right side was purple, the bruise spanning from beneath his arm to his belly-button; just holding up his shirt hurt like hell. Gingerly, he ran his hand along his ribs, gently probing for anything broken. He was thankful to find that nothing moved too significantly, though he knew that now it wouldn't take much for them to break. He was lucky he hadn't done any more damage when he had escaped Teyla and the others.

With his free hand he managed to find a roll of bandages in the first aid kit. Awkwardly he managed to wrap up his midsection, quite a feat considering he was practically one-handed. Hopefully strapping up the injury would give it enough support so that he could keep moving. Once he was done he was pretty sure the wrapping was achieving very little, but it was better than leaving his ribs to be jostled.

His wounds cleaned and wrapped, John returned his shirt to his shoulders. He then found a bottle of Tylenol in the kit and palmed a couple. It probably wasn't wise to take pain medication with a head wound, but when he weighed it against being crippled with pain and defenceless he decided to take the risk.

Suddenly, there came a thump from the adjoining room and John rushed out. He was half-expecting to find that Torren had fallen off the bed, a place which in hindsight, may not have been the most sensible place to leave a child unattended. Instead he found the toddler sitting there looking rather pleased with himself. He had thrown the now-empty bottle onto the floor, and was looking at John as if he should be congratulated. Instead, John smirked "All done, I take it?"

Torren giggled happily, apparently having forgotten the trauma of the last hour of being left alone and hungry. John found him a toy to play with while he worked out what to do next. He figured they couldn't stay there; whatever was in control of the Lantis personnel would soon figure out how to use the city sensors and track them down. In fact, staying still as long as he had had probably already helped them find him. They needed to go somewhere where they couldn't be found – say, for instance, a place where a certain scientist _still_ hadn't got round to repairing damaged sensors. "The East pier."

A destination in mind, John began planning a route and the things he and Torren would need. He emptied the half-packed bag he had found earlier, briefly wondering why Teyla had been packing one, and then repacked it with essentials. He also found a tablet PC on her desk and slipped that in the bag as well. Maybe when he and Torren were safe he could use it to figure out what the hell was going on.

He realised then that if he were carrying Torren he wouldn't have enough hands free to hold the two weapons he had acquired. After a minute or so of searching he happened upon a thigh holster that he quickly tied on. Finished, he turned back to the toddler. "Okay, little guy. How'd you feel about going on an adventure?"

Torren gurgled, and then reached out his arms in a request to be picked up. John obliged, scooping him back up with his less damaged arm. Both the shoulder bag and Torren were on his left side, overbalancing him a little, but it freed up his right hand to hold the stunner, the sidearm holstered as a last resort. There was a still a chance that Teyla and the others were still there – he didn't really want to hurt them.

Now ready, John unlocked the door and stepped back out into the corridor.

* * *

><p><strong>(Past) 10.05am – Gamma TowerQuarters Alpha83-T [Teyla's Quarters] **

"Now, what have I forgotten?" Teyla asked her son as she came to a pause. She had packed, unpacked and repacked the bag that she was preparing for Torren to take for his trip to New Athos that afternoon; trying to remember everything he needed, then realising she'd packed a whole load of things he didn't. Torren, who was sat in what John had dubbed his 'baby-cage', just gurgled as a reply.

Teyla gave a small laugh at her child's complete indifference to her predicament. She always got uncharacteristically flustered when it came to preparing Torren for trips to his second home; she wondered if she would ever get used to it. Of course she wanted her son to spend time with his father, and she knew that Kanaan would do everything he could to keep him safe, but she always became paranoid when it came to sending him off. He _was_ going to a completely different planet literally light years away after all; she was allowed to be a little worried.

She would never forget the day she stepped onto New Athos to find it completely deserted. It had taken her nearly a year to learn what fate had befallen them, and even now she had found them, her people were not the same. It had been so easy for Michael to take them away – could she honestly believe that past events would never be repeated? Would she walk through the gate in a week's time to find her people culled – Torren lost to her forever?

Teyla shook her head to try and dislodge the horrible thought, but once the seed had been planted her fear began to flourish. This was the part of motherhood she had been dreading since she had found out she was with-child. The Pegasus galaxy was a dark place and Teyla was a warrior fighting back against its dangers – not exactly the perfect place to raise a child.

But now, looking at her adorable son playing with an earth-toy Rodney had brought back from his leave for him, Teyla couldn't imagine a world without him. She would continue to fight until she made this galaxy the safe haven she desired for him; and until she made that happen, she would shield him with all the love in her heart.

Suddenly, she was shaken from her reverie by a beeping from her door. She abandoned the spare set of clothes she had been debating over packing and wandered over to the door control. "Hello, John."

"Hey, can I come in?" he asked with one of his best charming smiles. Teyla stepped aside and gestured that he could, and then returned to the now half-packed bag. John took one look at the disaster zone surrounding the relatively small pack. "Wow. How long's he going for again?"

"Only a week," she answered, deciding that she would pack the second spare set of clothes. Torren was a bit of a messy eater, he was guaranteed to need a clean set when his dinner missed his mouth.

"Really?" John raised his eyebrows in mock surprise. He was aware of her nervous nature when it came to sending Torren away, even though she usually hid it well when she was around the others. He had purposely shown up to provide her the support she needed but would never ask for. He could see just how distracted she was as she repetitively folded the same set of clothes several times. "He's going to be okay, you know. The Athosians will take good care of him."

Teyla blinked in surprise as the colonel practically read her thoughts. She finally stopped fussing over the clothes and sighed. "I know. I trust my people with my life, but I am also well aware that there are things beyond their control. There are too many unknowns in this universe that I cannot help but worry when Torren is out of my sight."

"You could say the same about Atlantis," John replied, gently leading her to a seat and sitting next to her. "Random things happen here that are beyond our control; there's always that risk wherever he is. All you need to know is that he's got the whole of this city looking out for him as well as all of your people. He couldn't be in better hands."

Teyla nodded slowly, and then smiled over at him. John always surprised her when he spoke like that. He would never allow anyone to see his own worries, but he could see the concerns in others and would offer comfort if he could. It was no wonder that he had earned the respect of the entire expedition, and not just for his heroism, but for his personality. He would always be a friend to her, even if sometimes she wished for him to be more, and she trusted him completely. "Thank you, John."

Again he smiled, and for the first time that day, Teyla could honestly say that she wasn't worried. As long as she had John Sheppard, there was no obstacle she could not overcome.

"Sheppard here," he said suddenly, dragging Teyla out of her comfort bubble. She realised he was talking to his radio and remained silent as she listened. "Surely you can find someone else? There's at least seven ATA's in the new recruits as well as the twenty or so we've already got – they can't all be busy." He rolled his eyes at whoever was on the other end of the call. "Hey, I'm busy as well…what? Fine…fine! Yeah, I'm on my way. Out."

"Who was that?" Teyla asked as John huffed irritably. The sensitivity he had shown her mere moments before had completely disappeared and she was dealing once again with a guarded soldier.

"Some scientists up in delta want me to fulfil my duty as human light switch. Apparently, it being my day-off just means I'm not doing anything," John looked sour as he dragged himself to his feet. "First Fredericks, then Woolsey, now this."

Teyla stood as well and gave his arm a reassuring squeeze. His annoyance melted a little and he smiled again. "Never mind, eh? I'd probably be going stir crazy by now anyway," he headed towards the door that opened at his command. "I'll try and be at the gate later; maybe I'll come to New Athos with you. Noon, right?"

She nodded, and with a wave he was gone. She stood there for a moment, trying to order her thoughts and keep her emotions in check. Then she returned to her previous task, callously tipping the bag upside down so that she could repack it while running the items passed the mental checklist in her head. It was better to keep herself occupied than to let her thoughts stray to the dangers of the galaxy; or to a certain lieutenant colonel.

In the twenty or so minutes between John leaving and the explosion in the delta lab that he was in, she must have fretted over the pack a hundred times. But it was instantly forgotten when the floor shook beneath her, despite the distance from the central tower. She tapped at her earpiece with a little more force than necessary "Teyla to Colonel Sheppard; what happened, John?"

A sick feeling settled in her stomach when he didn't reply. Some part of her instinctively knew that whatever had happened, John had been caught in the middle of it. Maybe Torren had picked up on her panic, or he himself had sensed it too, as he started crying from his crib. Torn between wanting to run off and help and staying to look after her child, Teyla picked up Torren to comfort him while opening up her radio to listen to the chatter.

"_This is Keller, I'm at the scene. It's lab delta29-B that's exploded. I've been told that there were people inside, but I can't get to them because of the rubble. I need combat engineers down here ASAP."_

Delta section was a big place, Teyla tried to convince herself. John could have been called to a different lab and was now too busy helping that he hadn't been able to answer his radio. Before, in any other situation, he had always kept her in the loop though – he would've called her back by now. Teyla rocked back and forth with Torren in her arms, trying very hard not to panic. She froze when she heard McKay confirm her fears.

"…_they called for an ATA user…I think…I think Sheppard's in there too."_

"No." Teyla whispered. Torren's crying grew louder as he reacted to his mother's distress. John had been with her only twenty minutes ago. He couldn't be…he couldn't be…

Teyla held Torren closer as she battled against her concern. She was a strong woman, a leader of her people; she needed to call upon that strength now so that she could logically think things through and decide on her next step. Of course she wanted to run off to the hot zone to try and help, but she couldn't leave Torren. She chewed her lip as she tried to come up with an alternative.

But then the decision was made for her. A wave of darkness covered her eyes, and suddenly Teyla was pushed to the proverbial back-seat of her own mind.

She was completely paralysed, her own body suddenly becoming alien to her; but she could see and she could hear. Torren had stopped crying and was now looking up at her with wide, confused eyes. Fear pummelled Teyla as she realised _something else_ was holding her child. She fought against her constraints, desperately trying to evict the other consciousness, but her efforts effected no change.

Suddenly, a strange voice sounded to her inner ear. It was not unlike when she connected with a Wraith, a familiarity that immediately doubled her fear. The voice was instructing her, or rather the being controlling her, to assume the identity of its host. She suddenly felt violated as whatever she was sharing her body with began casually flicking through her memories and thoughts as if she were simply a book to be read. Again, Teyla tried to stop the being, though she doubted she had achieved anything more than being a slight hindrance.

The being tripped on a memory of Torren, then glanced down to find it was holding the child in Teyla's arms. It assessed the child to be a hindrance, nothing more, and then placed him back inside his crib. As Teyla silently thanked the being for not hurting her child, it resumed its previous task of ransacking her mind.

The rifling abruptly stopped when another order drifted into her mind. The voice sounded angry, and Teyla felt the being inside her shy away from the strong emotion. Teyla felt as close to joy as she could considering her situation when she translated that there were people in Atlantis still free from the control that trapped her. Although now, she realised, that the being inside her was now going to use her to hunt down her friends.

"As the Voice decrees, so shall it be."

* * *

><p><strong>11.20am – Sigma TowerHolding Cell Zulu2-C **

"We are the Collective. Atlantis belongs to us."

"Well that wasn't in the slightest bit helpful, now was it?" Rodney sarcastically replied. The guard didn't react at all. Maybe Harvey had been right that talking to the zombie-marines was useless. "What happened to bad guys helpfully monologuing when you need them to, huh?"

McKay quickly grew bored with 'interrogating' the brick wall that was a prison guard and slouched down next to the gate tech. Harvey briefly threw him an 'I told you so' look but left the scientist to sit in silence and think. Rodney replayed the events of the morning, his brilliant mind trying to put the pieces together in a way that made sense.

He figured that it was probably some sort of possession or influence that was controlling the members of the 'Collective', though he couldn't figure out how or why. It must have happened around the time of the explosion, the timing was too coincidental for it not to be related. He cursed himself for not listening to the laptop thief the night before when she had been babbling about the lab. McKay hadn't been interested in the lab and as such had assigned it to Parsons and Volkov, two good scientists who were most likely now dead. Rodney couldn't believe that Sheppard was dead too though, he'd seen John come back from too many impossible situations for him to have gone out like that. There was no way the colonel was dead.

At least, that's what Rodney hoped. He dragged his thoughts back to the current situation. He scanned the prison cell again, more slowly this time. There must be something they all had in common to explain why they were all immune. He picked up on the different uniforms; there were soldiers, scientists, a doctor, a few combat engineers and a handful of _Apollo_ crew members who had decided to stay when the ship had left. Why were these people still normal?

Rodney could have kicked himself when the reason finally clicked. If he were alone, he probably would've, but with the others there he didn't want to admit it had taken him so long. "We all have the ATA gene."

Harvey glanced at him, and then scanned the room as well. He obviously drew the same conclusion. "So that's why we're not zombies." The gate tech paused, and then looked at Rodney in confusion. "How does that help us?

Rodney just smiled broadly as he noticed that a few faces were missing from the prison cell. "It means that there are still others out there trying to figure this out. Hell, they might even try a rescue."

Harvey caught Rodney's train of thought and smiled as well. They may not be as completely screwed as they thought. There were only two guards at the door; an air force major and a doctor could easily take them out. Rodney knew the code to disable the force field. All they needed was for Lorne and Beckett to show up, and they could be out of there in minutes. Then they could figure out what was going on, come up with a solution and have everything back to normal by dinner.

Yes, Rodney McKay could do blind optimism just as well as any lieutenant colonel.

His initial excitement began to fade however when no one appeared. Nearly ten minutes had passed since the grand revelation that help could potentially be on the way, and yet nothing had happened. If their wacky lives were really the sci-fi show they often felt like, the rescue would have arrived the moment he had realised; but this was reality and coincidences like that really didn't happen. The chances of the rescue happening were slim to none in the first place.

Maybe Rodney McKay didn't do blind optimism quite as well he thought.

Someone would have to come and get him eventually though. Come on, he was _the _Dr. Rodney McKay; the necessary component behind every solution to every hopeless situation that Atlantis found in the Pegasus galaxy. They needed him to pull the proverbial rabbit out of the hat and fix whatever was happening. The fact that Rodney didn't actually know how he was going to do that didn't change that he was needed if a solution was ever to be discovered. So where the hell was the damn rescue?

"Halt!"

Rodney whipped his head around at the guard's shout and grinned like a Cheshire cat. Taking cover behind the door frame was Major Lorne; with Carson and the laptop thief hiding just round the corner. The guards managed to keep them pinned with P90 fire that pitted the walls around them. The racket they were making wasn't good; it would only bring more of the zombie marines, but hopefully they'd be long gone before that happened.

Eventually there came a respite in the constant fire giving Lorne the chance to lean out of his cover and fire off two quick shots of his own. The Wraith stunner made the guards glow blue and spasm for a second, but then they were unconscious on the ground.

"Well that was easy." Lorne quipped as he stepped into the room. He kept his stunner trained on the downed guards and came forward to kick their weapons out of reach. He gestured for the other two to come in as well. "Get them out. "We need to get moving; fast."

Beckett nodded and entered the code McKay helpfully provided. The force field collapsed and the thick barred door slid open, releasing the imprisoned occupants. Two soldiers who had been in the cell with Rodney collected the weapons from the downed guards then turned to Lorne for instruction. Within moments they were running through the corridors of Atlantis.

"Where are we going?" Rodney asked Beckett as he kept pace with the entourage of convicts.

"The East pier, they shouldn't be able to find us there."

"'Shouldn't'?"

* * *

><p><strong>And voila, another chapter :P Please let me know what you think! <strong>


	4. Hunted and Haunted

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

Thanks to BMick, robvb2000, nanicom, JoeyLuv, BSBllseD, shirik, and sherry57 for reviewing! You are all wonderful and I'm really glad that you're enjoying this fic!

I thought I'd let you know that I have now finally finished the plot planning of this fic! I now actually know how this is going to end, which I usually a good thing to know when you're writing lol

Oh, just as a by the way, 'WPM' means 'words per minute'. I suspect you already knew that, but I thought I'd put it in just in case :P

* * *

><p><strong>Chapter Four -:- Hunted and Haunted<strong>

**(Past – The Day Before) 22.50pm – Central Tower/Lab Delta29-B **

"Sheppard, it's McKay. Can you meet me in delta section of the central tower? I think I'm going to need back-up."

"_What's happened?"_

"Some idiot has broken one of the Ten Commandments – 'thou shalt not steal'. Apparently that law only applies to humans when they're on Earth. Here in Atlantis, everything's up for grabs as far as this moron's concerned."

"_Who? And what did they nick?"_

"_My_ laptop – do you have any idea how long I spent updating that old thing so that it could handle the sheer volume of data I have to deal with? And I don't know who…yet."

"_Then how do you know it's in delta?"_

"Oh, I cobbled together a short range locator out of a subcutaneous transmitter and some wraith tech with an Ancient tracking device thrown in that I can trace using the city sensors which I had to update to only pick up on this signal, temporarily of course."

"_You put a GPS in your laptop?"_

"Yes, that's what I just said. Now can you hurry up please? I'm already here. The longer we leave my laptop in the hands of some novice who barely grasped eighth grade science the more damage they could be inflicting."

"_Why don't you just go in now if it's so important?"_

"What? By myself?"

"_Fine, I'm on my way. Five minutes."_

Rodney smirked as he ended the transmission. Whoever had stolen his laptop was going to get it both barrels now; once from himself and once from Sheppard who was going to be annoyed about being dragged away from whatever he was doing to deal with the problem. With a degree of patience the scientist waited in the hallway outside the lab with his arms crossed. The five minutes seemed to stretch on for eternity as McKay imagined the mishandling of his preciously customised computer.

"Okay, I'm here," Sheppard announced as he came round the corner, making Rodney jump. John felt like the bruiser friend of a bullied nerd in a high school quad whose sole purpose was to stand up for him. "Now who do you need me to beat up?"

Rodney rolled his eyes at John's sarcasm and waved his hand over the lab's door control. He felt a little silly when he found the thief to be a rather short and thin woman with mousy brown hair and glasses. But then again, Rodney had learned from Teyla not to judge a book by its cover – or a fighter by its height. Sheppard was snickering behind him, obviously rather enjoying himself. "You stole my laptop."

"I did?" the woman blinked, looking very confused at the red-faced man yelling at her. She then glanced around her at a number of Atlantis standard issue laptops all hooked up to several consoles. The consoles surrounded a large cylinder in the centre of the room that went from floor to ceiling like a pillar. Several HUD screens dangled from the ceiling, each displaying the Ancient data that was also rushing across the laptop screens.

"Yes, you did." McKay seemed to realise for the first time that he didn't recognise the woman – it wasn't uncommon for him to not know members of his own staff that had worked for him since the beginning, but he _really_ didn't know her. But she'd made herself right at home. "Who the hell are you?"

Again, the woman seemed slow as she got distracted by a beeping from one of the laptops. Rodney seethed when he recognised it as his own. "Oh, right. Of course you don't know me, nobody knows me; unless of course they were on the _Apollo_ with me then they would because we just spent the last three weeks together, but I'm new and you're not so, well…I'm McKinley. Miranda McKinley."

"Nice to meet you," Sheppard piped in when Rodney was too flabbergasted to answer.

"No it isn't!" he immediately countered, turning on the small woman. She didn't seem too concerned that he was so angry with her; she barely seemed to notice it as she started typing instead of paying attention. "You stole my laptop, you're completely ignoring me and now you're…you're…what are you doing?"

"Well, like I said, I'm new and I hadn't been given anything to do yet so I decided to explore a little and then I happened upon a lab a few floors up with this sweet Czech man who I spoke to and he said that there were always plenty of things to do and that some person called McKay had made a to-do list that I could use to find something to do," McKinley paused for her first breath. "I found this lab on the list that had yet to be properly investigated so I decided that I would well, investigate it, but I hadn't been issued anything yet so I borrowed a few laptops that weren't being used…"

"You mean stole. 'Borrowed' implies that you asked first," McKay interrupted irritably. McKinley just shrugged, her nonchalance annoying Rodney even more – if that were possible. She had already danced on his last nerve by simply talking so damn fast.

She continued as if he had never stopped her; her lips moving impossibly quickly. "It's quite fascinating really – this device is akin to a microscope but incredibly more powerful so that it can magnify things on a nanoscopic level. I haven't turned it on yet though; there's a whole bunch of firewalls and levels of encryption I've never seen before – your laptop was the only powerful enough to even begin to break them down. Instead I've been reading up on the experiment in the Ancient database…"

"It's just a microbiology experiment," Rodney dismissed, now remembering why the lab had been on his to-do list for so long. He never had had much interest for biology, his area of expertise being the far more mathematical and complicated science of physics. "Even the Ancients got bored and abandoned the project."

"That's not true," McKinley defended. "I'm only a part-way through the entry but I can tell you that this was far more than that. The Ancients found a nanoscopic culture of multicellular organisms with significant cognitive ability – how someone finds something that small I'm not entirely sure; but they managed to capture it and build this device in order to study it. They called the culture '_Alcoloniavarium' _which basically translates to 'hive colony' like ants or bees…"

Rodney wasn't listening anymore. He knew that now the investigation had been started it would have to be finished, but he had no intention of being the one to do it. And neither would McKinley. The lack of 'Dr.' in her introduction was leading him to doubt her qualifications. He didn't remember seeing her name on the new roster either – was she even a scientist? He waited with his arms crossed until the next time she paused for breath "You're not allowed to investigate a lab without at least one other scientist and a marine escort, so stop what you're doing and give me back my laptop."

"Oh." McKinley looked completely crestfallen at being evicted from the lab. Then she looked a little sheepish. "I can't. You're laptop is still running the decryption code – disconnecting it now could cause significant data corruption. I can leave it to run by itself though; it should be finished by the morning. Maybe I could come back then with someone else and finish…?"

"No." Rodney immediately refused. "I'll set a team to work tomorrow. Now get out."

McKinley fled the room with her tail between her legs; her expression utterly heartbroken. Sheppard gave her a reassuring smile as she left. He felt sorry for the poor girl; she wasn't familiar with McKay's method of dealing with people yet, and after that episode, he doubted she'd ever get the chance. "That was a little harsh McKay."

Rodney just shrugged as he walked up to his laptop and double checked that McKinley was telling the truth about it being impossible to disconnect. He was mildly impressed by the program she had running, but was too annoyed to give her any slack. "She had it coming – she broke the rules, stole my laptop and had the nerve to disagree with me."

Sheppard smirked. "You're just jealous that she has a faster WPM rate than you."

"Shut up."

* * *

><p><strong>11.40am – East PierStorage Area Foxtrot5-C **

The storage area they chose to hole up in was the perfect hideout, and not just because the sensors in the area were blind. The area where the sensors were down was big enough that it would take time for a manual search if the others so decided to do so; and also their little section almost completely inaccessible. There were only two entrances; the main entrance on the south side that led from a maze of corridors; and the auxiliary entrance that was hidden to the east side. It would make a good escape route if they were discovered.

Lorne was pretty pleased with the set-up. It was easily defendable with the few soldiers and weapons they had and was also big enough to house the twenty-or-so of them quite easily. It would do as a base of operations where they could figure out what the hell was going on and a way to fix things. Hopefully they could bring some control to the chaos.

The Major took a look around at the people gathered in the room; taking a headcount of all the people now looking to him for instruction. He had found himself the four marines he had wanted along with three lieutenants from the _Apollo_ and two soldiers from the air force like himself. At least now they had a fighting chance. He had also picked up nine scientists from McKay's team, a gate tech, two civilians and two medical doctors who were already checking on the injuries the others had received during capture.

There were twenty-five in total. Twenty-five vs. two-hundred-plus well-armed mind-controlled personnel. To say they were outnumbered was an understatement.

They were limited with weaponry as well. Lorne and the others had managed to acquire only four stunners including the two picked up from the prison guards; as well as two P90s and 9mils. He really didn't want to use those if he could help it. Enough blood had been spilt by friendly fire that day already.

First, they needed to secure the area. "Richards, Alvarez; take guard down the corridor of the main entrance. You'll work as an early-warning system to Lowe and Davidson who'll take position at the door. Jensen and Fuller do the same with the auxiliary entrance with O'Brien and Mendez on the door."

He received a series of crisp 'yes-sir's and the guns were split between them. Lorne couldn't hide the wince when a marine cocked a P90. He remembered a time when the sound had been a comfort, reminding him that he had the means to defend himself. Now all it did was remind him of what he had done. Would he ever be able to fire the weapon again? Would the guilt that currently weighed heavy on his conscious stop him from being the soldier he needed to be? Would it stop him from doing what needed to be done?

From across the room he saw Beckett throw him a sympathetic look. The doctor had seen his reaction and knew the struggle that was going on inside his head. Lorne really wanted this day to be over.

But in order for the day to end well, he needed information. He walked over to a cluster of people consisting of McKay, Beckett, the gate tech Harvey and the woman whose name he'd finally learnt to be McKinley. "What do we know?"

"You mean other than nothing?" McKay retorted. Lorne threw him a look that said he really wasn't in the mood for the astrophysicist's sarcasm. McKay had the decency to look apologetic; Lorne's expression telling him that he wasn't just in a bad mood. "Well, we know that 90% of the people in the city have been turned into zombies with guns that are trying to capture us for some reason. We know that only people with the ATA gene have been unaffected and that we were all briefly knocked out – again, we don't know why. We also know that all this occurred after a lab exploded with two scientists and Colonel Sheppard in it – a lab that _you_ were in last night."

Lorne picked up on the slightest hint of emotion that came out when McKay mention Sheppard. He suspected the scientist had come to the same conclusion as him but was refusing to admit it for the moment. Without anyone able to get to the hot zone to help he doubted that there had been any survivors. Right now, he was the highest ranking military officer on Atlantis, and it was up to him to fix the problem. He turned to look at McKinley at Rodney's accusatory tone.

McKinley shifted uncomfortably as all eyes turned to her. "I had barely scratched the surface when you and Colonel Sheppard came and evicted me, but from what I learned I can't see how it relates to what's happening. It was a microbiology experiment with a hint of social science thrown in. It was simply an observation platform for a nano-culture that I doubt could've survived all this time in containment. I don't even know what could have exploded."

"'Nano' – as in nanites?" Harvey ventured uncertainly.

"No, no. _Alcoloniavarium _was an entirely organic culture and occurred in nature," McKinley replied and Harvey relaxed a little. They had all drawn the connection to the Asuran replicators due to the robotic nature of the personnel, but after Major Lorne's run-in she doubted they were related. "The Ancient's simply found it, they didn't create it. They only took an interest due to the cognitive abilities of what should essentially have been single-celled amoeba. _Alcoloniavarium_ actually translates to 'hive colony' as each of the cells acted both individually and as a whole. It's quite fascinating really…"

"But you don't think that this alco-whatever is what's doing this?" Lorne interrupted, recognising a pending lecture when he heard one.

McKinley shook her head, though she didn't look entirely convinced. "We can't rule it out, obviously, but like I said, I don't see how the culture could have survived over 10,000 years. Also, in what I translated from the Ancient database there was no mention of a 'collective', a 'voice' or anything else."

"It's too much of a coincidence for it not to be related though," McKay added. "If I could get a hold of a computer or access a terminal I might be able to pull up some more information – get a better idea of what we're dealing with."

"I'll add that to the to-do list," Lorne replied. He was already aware that they'd have to leave the relative safety of their hidey-hole soon. They needed supplies as well as information, and they weren't going to get those by staying hidden. He turned to Beckett. "What about our immunity? Could there be a way to use that somehow?"

Beckett shrugged. "If it really is the ATA gene that's somehow protecting us there is nothing other than the gene therapy that could be used on the others. Most of the people out there have already had the inoculation but it didn't work. Trying to come up with an alternative treatment would take time, research and resources we don't have."

"Alright, so we'll stick with plan A – try and figure out what happened and find a way to reverse it," Lorne decided. "I'll take a team out to gather supplies and information; maybe grab one of the infected if we can, then come back here and decide our next step."

"Sir!"

Lorne snapped around at Lieutenant Lowe's hushed shout and closed the gap between them in seconds. "What is it?"

"Someone's coming."

* * *

><p><strong>11.40am – Omega TowerLevel 13 Section Romeo **

'Teyla' kept replaying the moment she had held the gun to the prisoner's head over and over again. For the briefest of moments; she had lost control. The host who's designation she had taken as her own had been strong enough to fight back. Something about her host was different – its mind was stronger, fortified and powerful enough to push against her control. Even now its consciousness was aware and screaming for freedom. It took everything she had to keep it at bay.

Part of her was glad for the challenge. When she had been released before she had easily taken control and integrated quickly with her host. There hadn't been a struggle. It had been almost boring; not worthy of her. This host presented a situation she had never faced before; the experience was far from boring. But it also presented the opportunity for failure. No one of the Collective had ever failed to assimilate a host before. She would be disowned and left to exist alone if she were to be evicted by her host. She liked a challenge, but the thought of being without the protection of the Collective was beyond her worst nightmare.

For now, at least, she had close to complete control. The body was hers to move, to use, to adapt as her own. Once the assimilation was finished she would no longer have to fight her host; its consciousness would be completely erased.

Earlier, when she had experienced her host almost winning out against her she had asked the Voice if she could erase the consciousness prematurely. Her request had been refused. Conclusive assimilation was necessary to create complete beings. They needed to learn everything there was to know from their hosts before they could evict the original consciousness. Once it had been removed she would be unable to learn. A gap in the Collective's knowledge and ability could result in its failure.

So she would endure and do as the Voice decreed. At this moment that meant that she had to repair her earlier mistake. The prisoner that escaped his execution was now her target and hers alone. She was to find him and eradicate the threat he presented to prove that she was strong enough to assimilate completely. The battle of wills she had engaged in with her host would be over soon; and she would be the victor.

She stalked down a deserted hallway and hid herself in a recess of the wall, shadows swallowing her whole. With a slight tilt of her head she connected herself with the one designated as 'Chuck' in the control tower. He was functioning as the eyes of the Collective as he studied a newly discovered device that monitored life signs within the city. He had identified two life signs that were not of the Collective. Somehow, 'Teyla' knew that one of them was her target. 'Chuck' informed her that the life signs were moving toward her position and an image of the immediate area's layout appeared in her mind's eye.

With the information now imprinted in her mind she disengaged from 'Chuck' – the better to concentrate on keeping her host's consciousness at bay. She could not afford another failure. She wouldn't allow one.

The target appeared at the end of the corridor; weapon first. He was being cautious; his eyes alert and pace slow as he gradually moved toward her position. She then saw why he was being so cautious. Her host immediately doubled her efforts to break free as she saw the other life sign he carried. The child.

She flinched at a particularly violent outburst from her host and instantly the target swung the weapon in the direction of the movement. He couldn't see her, but she could see that he was tense and ready should she reveal her position. She stilled her breathing as she had learned from her host, the cold metal of the P90 feeling good in her grip. She'd wait until he passed and end him with a single shot. She'd take the child as well – it could be useful as a bargaining chip against the other uninfected. She would prove herself.

"John!"

The word came from her lips, but she had not uttered it. Her target spun to face her, just about seeing her outline from her shadowy hiding place. She tried to claw back control, but her host's consciousness was even stronger than before. Her feet were moving of their own accord, forcing her out into the open. The weapon in her hand was lowered.

"Teyla?"

Her target moved to such an angle that the child was hidden behind him. His weapon arm was still outstretched, the stunner aimed directly at her. Her host was still managing to maintain control, but 'Teyla' pushed back, gaining enough ground to raise the weapon and twist her finger round the trigger. She focused all of her energy on the simple act of pulling the trigger.

"John…please…stop me…"

Emotions were battering against her as she continued to battle against the unnaturally strong consciousness. There was fear; her host was petrified of hurting the man and child in front of it. There was anger too, a red hot rage aimed directly at her for daring to use it as a weapon against its own. And finally there was trust. It trusted the man so completely; it trusted him with her child and it trusted him to shoot it.

"Please."

There came a flash of blue and 'Teyla' abruptly found herself hovering like a fly on the wall. Her host crumpled to the ground as her target took a hesitant step towards it. He then decided against helping it and continued off down the hall.

Her target had escaped and she was separated from her host. She could feel the anger of the Voice even as it kept her conscious through her connection to the Collective. She would not be able to return to her host while the stunner weapon's energy coursed through it. She would have been eradicated if it had not been for the Voice's intervention saving her from oblivion.

She watched, completely powerless and helpless in her natural form, as her host woke up and scanned around it. It then immediately climbed to its feet and ran to a door that opened when it waved a hand over the control. She followed it inside to find herself in a room like any other in the city. It only had one door though, which her host immediately locked. It then removed the control crystals and smashed them on the floor, effectively imprisoning itself.

The effects of the stunner's energy dissipated and 'Teyla' was pushed back into her host with a helpful shove from the Voice. It had obviously decided to give her a second chance; one that she promised would not be wasted.

The fight when she returned to her host's mind was significantly weaker than it had been before. She could feel it's exhaustion as though it were her own. She knew that if she were to catch up to her target now she would easily be able to quell its struggles long enough to complete the task; however that was impossible. In its moment of clarity, her host had locked them in the room with no hope of escape. There weren't even any windows for her to break and get out that way. No, she was totally trapped.

"Never mind," she muttered, catching her reflection in a mirror. It felt good to be in control again. "This will just give me some time to get to know you better. Then I can be rid of you for good."

* * *

><p><strong>11.55am – East PierStorage Area Foxtrot5-C **

"Freeze!"

John did as he was told. He even put up the hand that held the stunner in a sign as close to surrender as he could get, considering he had a baby in his other arm. Of course he could easily change the gesture back to being weapon's ready in a split second if the situation called for it, but he had a feeling the marine before him wasn't trying to kill him. "Easy, Sargent."

"Colonel Sheppard?" the marine, Alvarez, questioned uncertainly. He clearly looked uncomfortable pointing a weapon at his commanding officer, but didn't lower it regardless. John read from his behaviour that he wasn't like the others that had tried to kill him an hour ago. It was a relief, to say the least. Alvarez waited until Major Lorne and two other soldiers appeared. "Sir?"

"Hi Lorne." John nodded at his second in command and half-smiled. "You're not trying to kill me too, are you?"

"Colonel?" Lorne looked shocked and more than a little relieved. The Major took in his appearance with one glance and gestured that Alvarez and the others could lower their weapons. "We thought you were dead, sir. The explosion…"

"I'm just a little banged up is all," John indicated the head wound. "I was rescued by Keller and a few others before Teyla tried to execute me. How many others are normal?"

Lorne turned to head back down the corridor and John matched his pace. The marines returned to their vigil and the two soldiers followed behind them, taking their posts by the door. "Twenty-five, well, twenty-seven now. It looks like those with the ATA gene are immune from whatever's controlling the others somehow…"

"Sheppard! You're alive!" McKay declared unnecessarily as John entered the room. Several others looked just as happy about the news and John felt a little uncomfortable. He never had been very good at receiving attention. He decided to rely on his sarcasm to deflect it.

"Really McKay? Hadn't noticed."

Rodney rolled his eyes, managing to master relieved and annoyed at the same time. He was standing in a group with Beckett, a woman in a red civilian uniform and a gate tech he couldn't remember the name of. The scientist then noticed Torren for the first time. "Huh, so Atlantis is in the middle of a zombie apocalypse and you pick up a baby?"

It was John's turn to roll his eyes. He then reached into the shoulder bag, a difficult task considering Torren was practically perched on top of it. The woman stepped forward and took him off him, allowing John to get to the tablet PC he had stolen. "I also got a computer."

Rodney looked mildly impressed considering that no one else had so far provided one, but quickly hid it behind another comment. "Which is really useful because I'm here and actually know what I'm doing – but what were you going to do with it?"

"Play Tetris." John deadpanned. Rodney tutted irritably then slid down the wall so that he was sat on the floor. The woman who had taken Torren wandered off, taking the shoulder bag of supplies and the gate tech with her. John looked after her, eyebrows furrowed. He felt like he should know her, but like many other things from before the explosion, he was drawing a blank. "Who was that?"

"The laptop thief…McKinley something or other," McKay supplied from his post on the floor. He then looked up and studied Sheppard as if seeing him properly for the first time. "But you should know that. You spoke to her both last night and this morning…"

Suddenly Beckett was looking at him with growing concern. Lorne gave him a sideways look as well and John felt like a display at a freak show. Yeah, he was hurting, he was tired and he had a pretty large gap in his memory but he didn't feel he warranted the scrutiny he was now receiving. He tried again with the sarcasm. "I'm good. I just got blown up a few hours ago."

Beckett wasn't buying it though and he was quickly being guided over to a corner where he could sit on a storage container while the doctor set about checking his head wound. He managed to hide the wince that the movement of his bruised ribs caused – he didn't want to give them anymore reason to put him on the side lines when the action plan was decided later. As he patiently sat through Beckett's checks he caught sight of Lorne's expression. The despondent look in his eyes was one that John had seen before, both in other soldiers and in the mirror. It was a look that only the guilt of a friendly fire incident could instil. "What happened Major?"

Lorne blinked in surprise at the question. He had expected his CO to ask for a sit-rep and what his plan had been before his arrival, but instead his question implied something more personal. Beckett threw them both a glance before busying himself with being invisible. This was a conversation best had in private. Sometimes the colonel startled them all with his perception, but after nearly four years, Lorne shouldn't have been surprised.

Sheppard waited as Lorne read between the lines of his question. He could already guess what had happened considering what he had woken too. If he hadn't had a stunner when Teyla had stopped him in the corridor on his way here, he suspected he would've had to shoot her in order to protect her child. He didn't want to think about what could've happened if the choice of just stunning her had been taken away. Lorne briefly explained what had happened and it was just as Sheppard had suspected. It had been an accident, but from experience John knew that that was little comfort.

"He was a friend," Lorne admitted, his voice extremely quiet. "We served together before we came to Pegasus. I knew his wife and his kid as well. I'll tell them…"

"Let's think about that later, Major," Sheppard interrupted, briefly putting a hand on Lorne's shoulder. "For now, let's focus on fixing this. You have a plan, yes?"

Lorne nodded, grateful for both the understanding of his commanding officer and the much needed distraction. "Yes sir. I was about to assemble a team to go out on a supply run. We have little to no weapons and I suspect communications are now compromised. I was intending to target the auxiliary weapons cache in Omega tower. Seeing how well-armed the others are I'm assuming the main armoury will have been fleeced by now. I was also aiming to capture one of those affected to try and get a better understanding of what we're dealing with."

"I just came through Omega on my way here. It looked pretty clear, apart from Teyla that is," Sheppard reported. Lorne gave him a questioning look. "She caught up to me and I had to stun her. I think it's safe to say they've got access to the city sensors as well as communications. They'll see us the moment we leave; taking the weapons cache could be interesting."

"It's a necessary risk," Lorne replied. "If we don't leave we'll just end up sitting here in the dark."

"I agree. We'll also need to leave at least four soldiers here to guard the civilians. We'll leave McKay here with the computer too; hopefully he can shine some light on what's happening. When were you planning on leaving?"

"I was thinking now, sir."

"Excellent idea, Major."

* * *

><p><strong>11.30am – Central TowerStargate Operations **

"I cannot locate the prisoners."

"Clarify 'cannot locate'," the Voice turned on the one designated 'Chuck'.

"I was able to track them until they entered this section of the East pier," 'Chuck' pointed at a rather large section of the city map, irritating the Voice further. The section was too big for them to search effectively and continue to defend the key areas under their control. He also had groups of the Collective focused entirely on assimilating, an act necessary for them to completely usurp their domination over the city.

The assimilation process was taking too long. Before when they had infected every Ancestor in the city they had been able to take their time. They had been almost complete when the others that came through the ring had disrupted them. This time as they had had to divide their attention between the downloading process and keeping track of those immune to their reach their progress had been significantly slowed. It would be at least another four hours before the focused groups completed and erased their hosts' consciousness's, and even longer for those who were currently distracted. They were at risk of a second failure if they failed to assimilate entirely.

But it couldn't change that. The process would take as long as it would take and there was nothing it could do to speed it up. What it could do instead was remove the distraction that was slowing them down. They needed to round the escaped prisoners back up so that they could be properly studied and either brought into the fold or eradicated.

The Voice addressed all those under his command and gave his instructions. The Uninfected had become a problem. Soon they were likely to retaliate. All key areas were to be kept under constant watch. The Uninfected were to be stunned and detained.

The Voice purposely sought out the one designated 'Ronon' once it had given its last instruction. He had already developed his host's trigger-happy attitude and didn't agree with The Voice's decision to leave the Uninfected alive – of course, he would still do as he was ordered however.

'Ronon' stood guard at the auxiliary weapons cache in the Omega tower, reluctantly flipping his blaster from 'kill' to 'stun'.

* * *

><p><strong>You thought I'd forgotten about Ronon, didn't you? :P <strong>

**Please review!**


	5. Looters and Lieutenants

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

Thanks again go to my wonderful, awesome, fantastic, brilliant etc. etc. reviewers! Not only do you give my muse fuel and much needed ego-boosts, but more often than not you end up giving me ideas that save me from myself :P As such, I thought it was about time to give credit where it's due:

Special thanks to Questfan's review all the way back on chapter 2; you're comment about how many zombies were gonna get hurt and the fallout is what led to Lorne actually having some angst this fic :P Before that it was gonna be a miraculous 'well, at least no one got hurt…how many stunners do we have anyway?' – so major thanks for giving this fic some depth lol

On the same note; JoeyLuv's follow up comment on chapter 3 about Lorne led to it being a recurring theme; I will admit I was gonna be a lazy writer and ignore the issue until the epilogue; but you prompted me to actually look at it closer – so thanks as well for making me write better :P

And last but not least, sherry57's comment on chapter 3 about Teyla being unable to hurt Torren because of her motherly instinct led to me re-writing the entire Teyla-scene last chap – no she didn't hurt him in the original, but she did fight John while he was trying to protect him. I didn't think it worked that well at the time, so thanks for giving me another idea!

As you can see, your reviews are most welcome and appreciated and will most likely lead to me stealing…I mean, 'borrowing'…ideas in the future :P

I'm done filling my word count now – Enjoy!

* * *

><p><strong>Chapter Five -:- Looters and Lieutenants <strong>

**(Past) 10.15am – Central Tower/RecRoom Delta29-A **

"Checkmate."

"What? But I…you were…how the…?" Lieutenant Henson spluttered in shock. He studied the chessboard in front of him and then looked up into the rather smug face of Dr. Arrighetti. He should've known better than to challenge the genius Italian scientist really, but Henson had never been one to back down from a bet. He handed over his opponents well-earned winnings. "Man, I really suck at this game. Can't we play cards instead?"

"Depends on what you are willing to bet," the Italian said slyly as he packed away the chessboard. "I should probably warn you though that I am a brilliant poker player as well – not that that stopped you last time."

Once again, Henson was suckered in. "So you reckon you're better than me at poker as well huh? I'll take that challenge. I bet a day's coffee rations that I can beat you."

Arrighetti's smile widened. As a spectacular scientist he required coffee to function at his far higher intelligence level. There was no way he could risk losing his own, but against the young lieutenant? That wasn't really a risk now, was it? "Deal. Who else is in?"

A few others joined the table and the cards were dealt. If Henson was honest, and he generally was more so than necessary, he wasn't that great at poker. Maybe it was the fact that he wasn't afraid of losing that made him such an eager competitor, or maybe it was just the chance to prove his worth, he didn't know. He'd gained a bit of a reputation as a terrible gambler which meant he was never short of opponents that were positive they could beat him. His luck was no better than usual when he recieved his hand.

Suddenly, someone appeared behind his chair. "Good hand, Lieutenant."

Henson swivelled slightly in his seat to look up at his commanding officer. Sheppard was looking at his cards, just about managing to hide his smile at their terribleness. Henson grinned, going along with the bluff. He never had been good at that part – you know; the important part - of the game. "Thank you, sir. There's coffee rations riding on this game. Care to join us, sir?"

"Afraid I can't, Lieutenant, I'm needed elsewhere," Sheppard glanced over at the Italian who was still looking very smug. "Besides, I'd never risk my coffee against Arrighetti."

"You learnt your lesson last time then, colonel?" Arrighetti retorted. Sheppard cringed, remembering how much he had lost that game. He then gave Henson's shoulder a quick, sympathetic squeeze and left the room. Several other players at the table were now looking a little nervous. The pot had already reached a week's rations.

Henson wouldn't back down though. One thing he hadn't told the Italian was that he didn't actually like coffee and usually ended up selling his rations to McKay. Sure, the astrophysicist would be pissed that he frittered away _his_ rations, but he could deal with that later. All that mattered then was beating Arrighetti. His own grin widened.

He was just about to reveal his winning hand when all of a sudden he was thrown from his seat. The adjoining wall with the lab next door had been blown out by the explosion, showering rubble all over them. Henson coughed on the dust in the air as he pushed himself back up and onto his feet. He looked around him to see people in varying shades of shocked and injured; and instantly the soldier kicked in.

"This is Lieutenant Henson reporting from the hot zone – there has been an explosion in delta section of the central tower. There are multiple injuries; we need med teams now!"

"_Understood, we're co-ordinating a response now."_

He heard Amelia reply over the ear piece but he was already moving on to assess the injured. He found Arrighetti amongst the rubble that had been their poker table only moments before. He rolled the limp scientist over and felt for a pulse. He had been hit on the head, although from what Henson could tell it wasn't too serious. He moved onto another player who had a glass shard protruding from his chest. He couldn't breathe, every attempt culminating in a pained wheeze. "Is there a doctor here? I need a doctor!"

Dr. Keller then appeared out of nowhere by his side, her med bag already open. Thankfully she had been in the area responding to a stair-related incident before the explosion. She quickly packed the wound to stop the bleeding, but her face didn't look hopeful. "Check on the others; only tell me about criticals, go!"

Henson did as he was told and began moving around the room. It seemed that most of them had been lucky and had mostly suffered only cuts and abrasions. But then he got closer to the hot zone. He stepped out into what was left of the corridor, but couldn't get any closer. He could see a hand poking out from beneath the rubble. There was a foot, maybe eight feet further up. He really hoped that they hadn't once both belonged to the same person.

He confirmed there to be at least six dead; and that was before he could even reach the focal point of the blast. Keller once again appeared beside him; her gloves covered in blood. She seemed just as frozen as he did until her training kicked back in. "This is Keller, I'm at the scene. It's lab delta29-B that's exploded. I've been told there are people inside, but I can't get to them because of the rubble. I need combat engineers down here ASAP."

She was then trying to climb across the rubble, paying no heed to how dangerous it was. Henson quickly followed her, gripping her elbow when she slipped. She answered a call on her radio "No, I need you to prep the OR, if they're any survivors they're going to be in pretty bad shape."

"Hey! Get down from there! It's not safe!"

Henson turned at the shout to see a combat engineer standing at the bottom of the rubble. There were a few others around him, but nowhere near enough. He looked to Keller who seemed reluctant to turn back, but then the pair of them made their way back down. A handful of medical teams appeared and Keller was quickly preoccupied with co-ordinating them once they reached the bottom.

"Major Lorne, this is Greggs. The tower is safe, there's no need for an evacuation. We've got more engineers on the way; we'll begin digging ASAP," the combat engineer reported.

Henson took a step back from the scene and leant against an amazingly unscathed wall. He couldn't believe that literally five minutes ago he had been about to win a game of cards. All he could see was chaos and destruction around him and now that the professionals were there, he didn't know what he could do. He decided to go back to the RecRoom and work at keeping the survivors calm. At least there he would be out of the way but still doing something useful.

When he climbed back over and into what was left of the room he found Arrighetti to be sitting upright and leaning against a lump of wall. The Italian was staring at the now-dead body of the man Henson had found earlier, the glass still imbedded in his chest. He'd been sitting next to the scientist at the table. He had been new; less than two days in the Pegasus galaxy. Henson hadn't even learned his name.

"Che diavolo è successo?" the Italian muttered, reverting to his native tongue in his shocked state. He looked up at Henson as he approached and repeated the question. "What the hell happened?"

"We don't know doc, but we're gonna figure it out," Henson tried to sound as reassuring as possible, though he suspected he sounded just as lost. Arrighetti then slumped sideways, completely unconscious before he hit the floor. Maybe the head wound had been worse than Henson had thought. "Hey! Doc! Hey! Can you hear me? Hey, you! Dr. Nakahara!"

The Japanese doctor spun at her name, but then passed out as well. Henson was torn between getting up to see to her and staying with Arrighetti. Around the room a few others also hit the deck. "What the hell? Hey! Dr. Keller!"

Keller was busy concentrating on her ear piece, trying to get through to Dr. Beckett to give him the numbers of injured inbound. "Hello? This is Keller. I can't get through to Beckett. Rodney, is there a problem with the radios?"

Henson then stood up, confused as to what he should do. All around him was a disaster zone full of injured and spontaneously-unconscious people. What _could_ he do? He needed orders and direction. He tried again to hail Keller. "Hey! Doc! Where do you need me?"

Then everything went dark and Henson disappeared.

Instead, a being now designated as 'Henson' stood in his place.

He waited, completely still, as The Voice decided what his orders would be. He mentally explored his new body, secretly pleased that he had found a host so young and able. He couldn't wait to learn all that the soldier had to offer. At his master's command he began to download his host's thoughts and memories, his glee growing. But then there was something wrong.

On the floor to his left, a human was stirring. 'Henson' learned that the human had not been infected as the others had; a fact that left him greatly confused and intrigued. How could such a thing be possible? The Voice reasserted his will; his anger palpable as he revised his orders. The Uninfected were to be contained.

'Henson' crouched before the groggy human, head tilted curiously. He found it odd that such a weak-looking being could possibly deflect the influence of the Collective. The human was looking at him, just as confused. "L-Lieutenant? What happened?"

"How are you not of the Collective?" 'Henson' asked. 'Keller' was looking at him oddly, but was then distracted by another human waking up. He didn't care. He needed to know what made that human so different from his own host. Not-knowing was driving him mad. "Answer. How are you not of the Collective?"

"Lieutenant, I do not know what you are talking about. Are you feeling alright?"

The human reached out towards him, and 'Henson' was forced to act. He viciously back-handed the human across the face; rendering the already fragile man unconscious. It was a shame, to say the least. 'Henson' had always been an inquisitive member of the Collective; always wanting to learn and understand. Maybe he would have a chance to solve the puzzle later; but for now he was to do as the Voice demanded.

"_Take arms. Find them, assess them and neutralise them. Begin excavating the Origin. Our second genesis has begun."_

* * *

><p><strong>12.15pm – Omega TowerWeapons Cache Bravo67-AuxD **

The group of soldiers were literally shadows as they made their way towards the weapons cache. It was located at the centre of the tower with three entrances designed to make the room both accessible and defendable should the need arise. They had met no resistance on their way there, though Sheppard suspected that their approach had already been detected. The others would know their target by now, and when they attacked, they would be expected.

The strike force consisted of only five soldiers, one for each stunner they had; the four marines and two soldiers being left to guard the others back at the East pier. The five of them were then divided into three, each team targeting a door each. Sheppard was alone while Lorne and Captain Riley had a man each; they also had the secondary objective of securing a prisoner as well as taking the weapons cache. They had split up on the floor below and taken different stairwells; their attack timed as they were unable to communicate.

Sheppard came to a stop in a recess of the wall, crouching down to keep himself hidden. His bruised ribs protested from the curled up position, but he ignored the pain. From his cover, John had a clear view of the doorway he'd be taking. As far as he could see there were only two soldiers guarding it, though he suspected there were more hidden inside. He then checked his watch; the attack would commence in thirty seconds.

John adjusted his grip on the stunner; Lorne had been adamant that they only use the non-fatal weapons and John was inclined to agree that it was the best choice. It did mean that the guards with the others had no choice but to rely on P90s and 9mils though; and there was a strong chance that the mind-controlled others would take this opportunity to seek them out. Their numbers were divided and the Collective knew it – John just hoped that the blinded sensors had hindered them enough to protect the others. That's where he had left Torren. Teyla would never forgive him if something happened.

With a short shake of his head that abruptly reminded him of his concussion, he pushed the thought away. He had to stay focused – they couldn't afford to fail.

Three. Two. One.

Sheppard stunned the first soldier without leaving his cover; a good thing considering the other guard then opened fire with his own stunner. The energy blasts chipped the wall he was hiding behind, showering him with shards. He could hear the sounds of more of the wraith weapons discharging from the other access points. He briefly wondered why the soldiers were favouring the stunners when they also had P90s, but decided, for now at least, he should just be grateful.

He returned fire, achieving two rather spectacular misses before he finally skimmed the soldiers firing arm. It wasn't enough to take him down, but it stopped his assault long enough for Sheppard to get off a proper shot. The soldier then joined the first on the floor.

There came a pause as the other teams took down their guards as well. Surely it couldn't be that easy. Sheppard cautiously creeped out from his cover, his weapon held ready. As he approached, he was well aware that he was an open target, but still, no attack came. At the doorway he quickly ducked to the side of the frame, trying to peer into the room. He kicked the gun away from the nearest fallen soldier, but couldn't reach the other.

The weapons cache was shrouded in total darkness; its position in the centre of the tower preventing any natural light from the windows getting in while the lights were out. Sheppard couldn't see a thing – but he still had to go in. He took a careful step around the door frame, barely an inch into the room.

A sudden light emitted from a P90 torch that Lorne had thought to bring with them. He flashed it around the room, allowing John to see the fist just before it connected with his face.

The blow sent pretty lights and colours dancing before his eyes, disorientating him completely. His already frazzled brain struggled to stay lucid as his limp body promptly hit the floor; his stunner flying from his grasp. Wraith stunner fire recommenced, battering his confused senses with light and sound. The pain was immense, slowing down his reactions and instincts. He then found himself being hauled up by someone much taller than himself. Then that someone hammered a punch into his gut, doubling him over.

He couldn't breathe; the air from his lungs expelled by the blow. Coupled with his concussion he thought for a moment he was going to throw up on his attacker, but by some miracle he managed to keep his breakfast down. Before his attacker made another move John had the sense to push himself away. His vision was coming back, though it remained hazy and unfocused. Even semi-blind his attacker was unmistakable though. Ronon.

_Oh crap._

The large Satedan came at him again; completely oblivious to the gun fight happening around them. Through some divine intervention he managed to block the first swing, but he knew that he couldn't beat Ronon even on a good day; and John was nowhere near 100%. The second blow connected with his already tender ribs and John felt something give. He didn't even want to think about the damage the hit had caused, but the pain was telling him that it was serious.

His ribs were on fire; his head felt like it was about to explode and he could feel fresh blood on his face from the reopened head wound. He could barely breathe, let alone fight back. Ronon was going to beat him to death.

He was relieved when what he suspected was a friendly fire stunner blast whisked him away from the land of the conscious.

* * *

><p>Major Lorne and Lieutenant Davidson approached their door with extreme caution, Lorne taking the lead while Davidson watched his back a few paces behind. They had taken out the two soldiers guarding their door with ease – something that was making Lorne very edgy. He quickly hid himself to one side of the door frame and gestured for Davidson to do the same opposite.<p>

He then tried to peer into the cache, but the lights were out, shrouding the entire room in near-blackness. He was glad he'd thought to bring a P90 torch with him and quickly pulled it out of his pocket. While still hidden behind the door, he flicked it on and sweeped it across the room.

Then all hell broke loose.

He caught a glimpse of a room full of soldiers, and then suddenly the room was full of bright blue flashes. Lorne was forced to duck back behind the frame as the blasts chipped the metal where his face had been seconds before. He fired blindly into the room, glad that he was armed only with a stunner and couldn't cause any more harm than he had already that day.

He was also glad that the others seemed to be only using stunners as well; even if he didn't understand why. Did the Collective only want to capture them? And if that was so, then what else did they have in mind for them other than death?

But that didn't relate to the immediate situation and Lorne pushed it to the back of his mind, instead trying to focus on the mission. It felt worse than betrayal to have to fire upon his own men, but if truth be told, there was no other choice. He decided to use the darkness to his advantage and crouched down low; sneaking around and into the room, keeping himself hidden in the shadows. He kept moving as he fired his weapon, making it difficult for the others to track his position. Using this method he managed to thin out their numbers significantly, allowing him a moment to pause and take stock.

Davidson was still pinned at the door, a fact that by his expression Lorne knew was annoying him greatly. Captain Riley and her Lieutenant had made it into the room and were employing a similar tactic to himself; together they were making quick work of the ambush. Then Lorne caught sight of his CO, and cursed. Sheppard had managed to pick a fight with a very angry looking Satedan, and it was pretty obvious that he wasn't winning. Ronon's attacks were brutal and Lorne could see that the colonel didn't stand a chance.

Lorne made a snap decision. He shot his CO.

He knew the stunner blast wasn't fatal and that in all honesty the act had been a mercy, but pulling the trigger still struck a chord with the guilt-ridden soldier. With every man he stunned he could see Sargent Walter's face looking at him accusingly. He had to snap out of it. He had to bury it until he could deal with it later. But the guilt wasn't giving him a reprieve, and he doubted he deserved it anyway.

Ronon grew uninterested with his now unconscious opponent and drew his blaster. Flashes of red joined the blue, the gunfight taking on a new level of ferocity. It took more than one direct hit to take the Satedan down, and even then Lorne wasn't positive that he was out cold.

Once Ronon fell the others soon followed. The weapons cache fell into silence following the previous cacophony. Lorne slowly stood from his cover and took a look around him. The ground was littered with stunned soldiers, bringing back memories of a tour Lorne would rather forget. The rest of his team came out as well, looking to him for instruction.

"Davidson, check on the colonel, Riley and Mendez, start collecting up weapons, walkies and TAC vests along with anything else you think might be helpful. And make it quick, we need to be long gone before they send reinforcements."

He acknowledged the chorus of 'yes sirs' that followed, and then focused on his own task. He stepped over a few soldiers and came to a crouch next to his Lieutenant. Henson laid there, unconscious and a little pale, a cut on his forehead from the explosion and a poorly wrapped bullet hole in his arm from their run-in earlier. The young soldier was a member of Lorne's team and the major had to admit that it was for selfish reasons that he had selected him as their prisoner. He wanted to get Henson medical help for the wound he had inflicted – maybe that would alleviate his guilt a little.

"Sir, the colonel's in bad shape," Davidson reported from the other side of the room, snapping Lorne from his reverie. Even from his distance he could see that Davidson was right – Sheppard was even paler than he had been earlier and his breathing was uneven. Ronon had really done a number on an already injured colonel.

"We'll get him back to the doc ASAP. Captain, are you ready?"

"Yes sir."

"Alright then, let's move."

* * *

><p><strong>12.30pm – Central TowerStargate Operations**

Now the Voice was more than a little angry. The Uninfected had succeeded in taking the weapons cache despite the ambush it had arranged the moment 'Chuck' had reported their likely target. It had also sent a team to begin searching the East pier where the life signs had re-appeared, but they had turned up nothing.

The humans were nothing if not akin to cockroaches – a race of insects it had learned of from its host. Apparently the creatures were very difficult to kill, or as in this case, capture, much like the humans it compared them to. They would be fascinating to study later once it finally had them within his grasp. Yes, it had some very interesting ideas for them.

It had also discovered that one of its kindred had been taken. The very thought of such an act made its blood boil; although, it would probably work out in their favour.

As soon as the one designated 'Henson' awoke; they would know exactly where the humans were hiding.

* * *

><p><strong>12.30pm – East PierStorage Area Foxtrot5-C **

_Well, that was weird._ Lieutenant Henson thought groggily. He remembered being in the middle of the hot zone surrounded by the dead and dying, and then…nothing. He really hoped that he hadn't fainted; he'd never be able to live it down.

He was confused when he found himself lying on solid ground rather than a soft infirmary bed. Maybe he had fainted at the hot zone and they just hadn't got round to moving him yet – there were far worse off people than him, he was well aware of that. He twitched slightly, testing his tired body. He felt like he'd run a marathon without warming up first, his entire body feeling physically exhausted. His head hurt as well, and he was cautious when he opened his eyes.

"He's waking up." Henson recognised the Scottish twang of Dr. Beckett. The doctor was wrapping his left arm – when had he hurt that? Maybe he was in the infirmary after all; they'd just run out of beds or something. Gradually the room came into view.

Definitely not the infirmary. It wasn't the hot zone either. What the hell had happened?

His confusion and panic doubled when he realised both his hands and feet had been tied. He struggled against the restraints and immediately found himself being held down by both Beckett and Major Lorne. He recognised Captain Riley hovering over him with a wraith stunner aimed at his chest. "S-sir? What the hell is going on?"

All three of them shared a look that Henson couldn't read. Was this a prank? If it was it really wasn't funny and was totally inappropriate considering the explosion. But then again, had that even happened? He didn't remember getting drunk last night but he was well aware that he was a lightweight; had he imagined the whole thing? Maybe he should book an appointment with the new psychiatrist…

"I think it's him."

"Are you sure? He could be acting."

"I don't think they _can_ act, lass."

"What are you taking about?" Henson tried to pull himself upright; he didn't feel all that dignified on the floor, but he was again pushed back down. Why weren't they explaining anything? _Answer the damn question!_ "Sir, I don't understand what's going on!"

"It's him."

"Do you reckon it was the stunner? Maybe the others are back to normal as well…"

"Get McKay over here, he said he knew something earlier, maybe this is related somehow."

Henson felt extremely left out of a conversation he was pretty sure was about him. They spoke about him as if he wasn't even there, and it unnerved him as well as annoyed him. Why wouldn't they just answer the question? "Could someone please tell me what is going on?"

"It's alright Lieutenant, we're going to figure this out." Major Lorne finally addressed him. He was the only one there who seemed convinced that he was indeed himself. Captain Riley still had her finger on the trigger, though he knew she'd never pull it without the major's permission. Dr. Beckett had disappeared and was quickly replaced with Dr. McKay. "He's back to normal, doc."

McKay frowned, studying him like a laboratory sample. Henson was immensely creeped out. Seriously, when had he not been normal? "I'm sorry, major, but it's only temporary."

"What do you mean, 'temporary'?"

"Amazingly, exactly what I said. Would you like the dictionary definition? Temporary, as in, not permanent," McKay explained with his usual sarcasm. He dialled it back a bit at Lorne's expression. "Whatever was in him before will reassert control soon and then he'll go back to being just another zombie again."

'_Zombie?'_

"So what? We keep stunning him? It wore off really quick, we'd have to keep doing it every ten minutes…surely that's not healthy?"

"We'll have to get Carson to sedate him until we come up with a proper cure. I must admit that the stunners having a similar effect to what the Ancient's used is quite fascinating. I'll talk it over with McKinley…I think I have an idea…"

"That's great doc, you go do that," Major Lorne dismissed McKay and the scientist took the hint. Riley picked up on his tone as well and cautiously backed away, leaving him alone with Henson. To say the lieutenant was freaked out was an understatement, and the expression on his superior officers face was not easing it any. "I'm sorry, Lieutenant, we're going to have to put you out for a while. Don't worry, though. By the time you wake up we're going to have everything fixed, I promise."

"I-I don't understand, sir."

"I'll explain it to you later. Goodnight, Lieutenant."

And just like that; Lieutenant Henson was swallowed by darkness.

* * *

><p><strong>Woot! A next day update! <strong>

**I hope you enjoyed and please, please, please tell me what you think! As I said earlier, your comments are necessary to stop me killing this fic by accident :P**

**See you next chap!**


	6. Tales and Translations

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

Many, many apologies for the incredible lateness of this chapter…once again Morrisons supermarket has become my second home where I've been practically working full time. To make up for it I am now writing this in the middle of the night, running on energy drinks after a 11.00-21.00 shift on a checkout…sympathise, and forgive pretty please :P

Also, many, many, many, many times a million thanks to everyone who has reviewed, alerted, favourited and/or read this fic do far; I cannot even begin to tell you how awesome you all are and I thank you for your patience…

Enjoy!

(Oh, and I am not scientifically minded in any way so a lot of the following is me making shit up – please suspend disbelief for a short while :P)

* * *

><p><strong>Chapter Six -:- Tales and Translations<strong>

**12.10pm – East Pier/Storage Area Foxtrot5-C**

"I still don't understand why you're going," Rodney muttered irritably. "By your own admission you _were_ blown up two hours ago."

Sheppard threw him a look before returning his attention to the blueprints McKay had pulled up on the tablet PC. Lorne, who was standing beside him, shifted slightly as if he agreed with the scientist but wasn't inclined to disagree with his CO.

This is what John had been afraid of when he'd let slip his memory loss earlier. He hated waiting on the side-lines while he put his men in harm's way; especially when he knew he was able enough to do it himself. He'd hidden his bruised ribs and managed to act as though the concussion wasn't so serious just so that he could be involved. Honestly, he'd performed rescues on hive ships with worse injuries. "I'm fine, McKay."

"If you say so…" Rodney recognised Sheppard-stubbornness when he saw it. He backed away from the tactical planning session to stand next to Beckett. "He's not 'fine', is he?"

"Not by a long shot," Carson agreed.

"Can't you stop him?"

"Already tried," Carson sighed, sounding just as concerned as Rodney. "Normally I'd restrict him to light duty on medical grounds, but in the current circumstances my rulings don't seem to have much by way of merit. I suspect we'll be able to say 'I told you so' when they get back though."

"As long as they come back."

Carson caught a hint of emotion underneath the irritated tone that surprised him. Before he had been cloned by Michael he had left behind a far more cynical and closed-off Rodney than the one that now stood before him. He couldn't believe how much his best friend had changed; and for the better. "Aye, they'll come back."

The tactical meeting seemed to be finished and John came over to hand back the computer. Lorne was busy filling in the others and giving the soldiers left behind their standing orders. Rodney continued to glare at the colonel. "For Christ's sake, McKay, I told you, I'm _fine_."

Neither McKay nor Beckett looked convinced.

John rolled his eyes and then gestured in the direction of McKinley who was busy entertaining Torren. "Can I trust you to keep him safe while I'm gone?"

"Of course." Rodney snapped indignantly, and then did a double-take. "That is if by 'me', you mean somebody else who is not preoccupied with figuring out what the hell is going on and how we're going to fix it, then yes." Sheppard glared at him. "If you're so concerned then why don't you stay here instead of going off and doing you're soldier thing!"

"Let it go, McKay." Sheppard warned. He tapped the computer in Rodney's hands. "You do your science thing, I'll do my soldier thing. Maybe we'll all get out of this in one piece, okay?" Rodney gave a reluctant nod. "Good. We'll be back in fifteen minutes, tops."

"You better be." Rodney muttered as Sheppard turned and left with the others. Carson gave his shoulder a reassuring squeeze and then continued on his rounds of the injured scientists left behind. He crouched in front of an Italian with a nasty head wound that had apparently been right next to the explosion when it had happened and set to work. Rodney slid back down the wall and perched the tablet on his knees as he continued his own work.

After a few minutes McKinley came and sat next to him, leaving Torren with Dr. Nakahara, the Japanese medical doctor, who was singing to the contented toddler in her native tongue. "Have you found anything out yet?"

"What, you mean in the two minutes since I started looking?"

"You are _the_ Dr. Rodney McKay, right? I thought that's all the time you needed," McKinley replied with a smile. She had managed to both goad and compliment him in the same sentence, and despite their first meeting, McKay found himself liking her. Well, at least hating her a little less anyway.

"Well, yes, I am, and usually, but…" Rodney stopped and tapped the tablet screen a few times to bring up the power distribution grid. "I've figured out what caused the explosion. Zelenka's been complaining even more than usual about these weird power fluctuations that started a couple of days ago. I was meant to be fixing them which I why I was monitoring power levels at the time. It was lucky I pulled the ZedPM and switched to back-up generators or the explosion could potentially have taken out the whole tower. When the device in the lab was turned on there was a massive power build-up that when it reached critical mass it, well…exploded."

McKinley shifted slightly, uncomfortable on the cold floor. "Do you know what caused these fluctuations?"

"Not yet, but I'm leaving that investigation until _after_ we've fixed this mess. I'm working on the more important problem of what has turned 90% of the base into zombies. I'm running keywords like 'collective', 'mind-control' and even 'zombies' through the Ancient database, but the processor in this thing is pathetic and the search is going slowly. I was going to try some synonyms as well in case it translated differently…"

McKinley sat bolt upright, making Rodney jump. "I'm such an idiot."

"I'm not going to deny that, but do you mind telling me why?" Rodney retorted. He yelped when she suddenly ripped the computer from his hands and started tapping fervently. "What are you doing?"

"How could I miss that?" McKinley began muttering in self-rebuke, still attacking the computer in annoyance. Rodney grabbed a hold of one of her hands, stopping her mid-stab and making her look at him. "I just took the literal translation; '_colonia' _is similar to _'colloqui'_ and _'cultu'_ which can also be translated as 'commune' as well as 'colony' which in some languages is a synonym to…"

"Stop, I don't need an etymology lesson," Rodney interrupted. Was this what it was like for Sheppard and the others when he explained things? He really hated not being the one in the know; it was a situation he found himself in rarely, but when it happened it left him feeling more than a little inadequate. He was smart enough to pick up on the similar sounding of the words though. "'_Colonia'?_ So now you're saying that the experiment _is_ related?"

"More than that; it's so obvious!" McKinley got out of his hold and continued her assault on the computer. "_'Alcoloniavarium' _can also be translated as 'collective'. The explosion must have released the culture somehow; maybe they're parasitic and require a host or…"

"I told you it was more than a coincidence," Rodney interrupted, trying to claw back some of his genius credit that was currently being stolen by a civilian. Seriously, she didn't even have _one_ PhD. "But how did they survive all this time if they need a host as you say?"

"I don't know; I had only made a dent into the database entry last night. Maybe there's more to them than I thought. I'll keep reading the entry and see if there isn't something helpful we can use against them or something…" she trailed off as her attention once more focused on the computer, effectively ending the conversation.

Rodney blinked, and then leaned back against the wall. He felt incredibly obsolete.

* * *

><p><strong>(Past) Over 10,000 years ago - SolarisAtlantis **

"Did we not perform adequately?"

"Oh no, it's not that," Phadara immediately backtracked; disconcerted by the cold stare she was receiving from her own creation. The female Asuran replicator tilted her head slightly, though her eyes never left Phadara despite the fact they were walking side-by-side. "No, Ilya, you and the others completed your tasks to perfection and within the dedicated time frame it's just that…"

"You frightened the humans." Phadara's assistant, Salem, unhelpfully supplied. She threw him an irritated look and he instantly fell back in step with the others.

Ilya was learning human expressions, and had recently mastered 'thoughtful'. She furrowed her eyebrows and added a slight pout for good measure. "I do not understand. Did you not create us to be weapons? And are weapons not meant to frighten others?"

"Yes, that is true, weapons are meant to frighten the _enemy_ in order to dissuade them from attacking us for fear our retaliation. They are not meant to frighten the charges they were designed to protect," Phadara explained as they neared that planets Stargate. "You're social integration is progressing rapidly, however I fear you may never fully assimilate with the humans."

"You designed us to fight the Wraith, not make friends with the humans." Ilya pointed out matter-of-factly. She gestured at her fellow replicators and then at the freshly reconstructed human settlement behind it. "These _additional_ tasks you are setting us are slowing down our weapons production and preventing us from fully immobilizing an efficient fighting force. It makes us wonder if these _distractions_ are on purpose."

"Of course not!" Phadara denied, a little too quickly. Ilya raised her eyebrows in a pretty good impression of disbelievement. Phadara turned away from the accusation in her creation's gaze and busied herself with dialling the Stargate. They had left Atlantis only a few hours prior to help rebuild a human settlement on Solaris that had fallen victim to the Wraith. Phadara had brought along Ilya and four others to speed up the process and also to see how well the replicators could blend with the humans. It hadn't gone well. "I simply believe that learning social interactions could help you better fulfil your potential."

Ilya was still giving her the unconvinced look; a look that she doubted the machine would've learned if it had not been for the excursions Phadara kept taking them on. The Stargate activated with its magnificent explosion of blue before settling into its eerie yet beautiful vertical pool. Phadara stepped through the wormhole first and entered out into the grand gate room of the city.

She took a few steps in, and then paused, looking up at the control room. She was surprised to see the city's leader, Kotor, as well as his two advisors, Shalira and Calowael, standing at the consoles. The three of them were rarely seen outside the High Chamber, let alone completing tasks better fitting the lower grade technicians. Kotor then stepped up to the control room's perch and looked down at her.

Behind her the gate shut down, the others having joined her. Salem nearly walked into the back of her, then followed her line of sight. He appeared just as surprised as she did to see the three highest members of their society. The five replicators simply stood and waited for their next instructions. Phadara called up "Councillors, it is rare to see you up there!"

She received nought but a steady stare in reply.

"Councillors? Is something the matter?" Phadara questioned, concern furrowing her features. Ilya looked to her, mimicking her expression as she picked up on her creator's tone. Kotor continued to stare, and Phadara grew irritated. The man had always been haughty and aloof, but this was taking the mick. "We have returned from Solaris; the Asurans worked well… would you like us to give our report?"

Ilya watched the exchange curiously. She had learned of the High Councillors self-important personality and had heard Phadara complain about him many times; but she had also picked up on his unusual behaviour. There was something distinctly different about him and the others, and it was putting her on edge – tension being another emotional state she had observed from the humans. She communicated the emotion to the others without speaking and they confirmed their similar conclusions.

"High Councillor Kotor, I ask of you to ans…"

Something odd found its way into a handful of Ilya's nanite cells. She identified the foreign particles, easily eradicating them and preventing the spread of them to the rest of her. She then turned to her creator to find out what had prevented her from completing her sentence. Immediately Ilya identified the odd posture and look of Phadara that she had witnessed in Kotor. In milliseconds she had put two and two together – the foreign bodies had infected their creators.

"What does the Voice decree?" Phadara, or rather the nano-particle possessing her, asked of the High Councillor. Kotor looked from her to Ilya and the others, his blank expression melting into confused irritation. Ilya translated that to be a bad thing. She looked to Jadah, the male replicator on her left, their hands reaching for the weapons their creators had reluctantly allowed them.

"They have failed to assimilate."

Kotor stated coldly, giving Phadara an accusatory stare. Whatever was controlling her looked contrite at the allegation, and then turned to analyse Ilya. "They are different from those who dwelled in this city. They are…machines."

"They pose a threat to the Collective. Destroy them."

"As the Voice decrees." Phadara drew her own weapon and immediately fired at Ilya. Obviously the pathetic blue stunner blast had no effect on her, but it was the first move that allowed the replicators to retaliate in self-defence. The gate room was suddenly full of blue lights and scorch marks as they exchanged shots. Phadara and the others didn't stand a chance.

Less than a minute passed before the only ones standing were Ilya, Jadah and the three other replicators. Their creators lay around them, merely stunned – their programming would never allow them to intentionally harm them. Ilya took charge "Remove their weapons and secure them in the conference room. I will activate the city lockdown to limit their movements."

The others immediately did as she commanded in total silence. She climbed the steps to the control room, skilfully stepping over an unconscious Shalira to take her place at the main console. At the touch of a crystalline button the alarm sounded and every door and window in the city slammed shut. The doors would open at their presence though; they could override the command to allow free passage for themselves.

Her own task complete, she went to the conference room where the others had efficiently secured their possessed creators in less than two minutes. Jadah stood at her arrival. "What should we do?"

"This presents a unique opportunity," Rydick, another male replicator, quickly replied as he also stood. Jadah flashed him a warning look, but he was ignored. "We could leave now and finally focus our energies on building the weapons needed to defeat the Wraith – fulfilling the very purpose we were created for."

"But we cannot leave our creators like this," Tallina, a female replicator argued. "We were created for others purposes besides defeating the Wraith…"

"Like helping the _humans_?" Rydick emphasised the last word as he had heard Phadara do when she spoke of someone she disliked.

Tallina blinked in reaction to the venom in his tone – she hadn't quite mastered flinching yet. "Yes, like helping the humans, protecting them _and_ our creators from _any_ enemy; not just the Wraith. We have to help them – identify what is controlling them and eradicate it as we did from our own cells. _That_ is what we are programmed to do."

All eyes turned to Ilya. Honestly, she could see both sides – it would be more efficient for them to allow the removal of their creators and their constant distractions to allow them to fulfil their primary directive; however they were also not allowed to harm their creators…did that include _allowing_ harm to come to them?

"What…what happened? Ilya?" Phadara pushed herself upright, her eyes widening as she took in the scene around her. Her fellow Atlanteans were still unconscious, surrounding her on all sides. The only ones standing were the replicators. She drew the only conclusion her blanked mind could come up with and fixed an accusatory glare on her creation. "What have you done?"

"What have _we_ done?" Ilya reacted in a very humanlike way, masterfully recreating defensive indignance. She mimicked annoyance and allowed the learned emotion to play on her features. The others looked just as offended, although none of them were as skilled as her at being human. "_We_ have done nought but defend ourselves!"

A flash of blue ended the conversation. Ilya glared at Rydick who still had his weapon raised at Phadara. "She is still infected."

"I am aware of that," Ilya rolled her eyes – another habit she had picked up. She crouched before Phadara's unconscious form and slid her hand into her creator's forehead. She probed her mind to learn of the possessive being. Once complete she stood again and addressed the others. "The weapon's energy discharge appears to disrupt the connection between the foreign particle and the host allowing them to return to their normal selves temporarily. The particle is evicted from the host in a dormant state but remains as part of the collective."

"It should be possible to create a city-wide pulse at a frequency that would render every particle dormant and prevent them from re-attaching to the hosts," Tallina proposed. "We would need to contain them quickly though; I suspect they will recover rapidly."

"Or we could just leave them as I suggested earlier," Rydick pointed out. "Our creators do not trust us; you saw how Phadara reacted…"

Tallina interrupted him forcefully. "She drew a logical conclusion."

"No, she accused us of something we didn't do – they all will eventually. They will find an excuse to terminate us once we have either fulfilled our purpose or proven to be more than they can control," Rydick continued regardless. "Already they try to prevent our progress. They 'fear' us. Human history proves that this 'fear' leads to discrimination and war. We can pre-empt their inevitable attack right now."

Again, Ilya found herself under the expectant gazes of her fellow Asurans. It was true what Rydick claimed; she herself had already seen the signs and had called Phadara out on them before. It would be so simple for them to return to their home world and leave the Atlanteans to their fate. But still, some part of her; probably her base code, insisted that she not allow that. Inaction could effectively kill her creators – action could save them. Though a choice had been presented, she truly had none. "We will help them."

Rydick tutted; he wasn't far behind her on developing human characteristics; while the others easily went with her decision. Tallina tilted her head as she communicated with the city's mainframe. "I have accessed the database. The foreign particles are from a nano-culture called _Alcoloniavarium_. There is a device in the tower that will attract, trap and contain them for future study once they have been disconnected from their hosts. It may require repair."

"We will need to separate and spread out in the city in order to create a pulse that will reach everyone," Jadah added and Tallina nodded in agreement. "We can emit the energy from ourselves at the required frequency."

"Let us do this before our creators awaken again."

* * *

><p><strong>12.25pm – East PierStorage Area Foxtrot5-C **

"The replicators solved the problem in under an hour – they're nothing if not efficient."

McKay finished his cliff notes version of the database entry McKinley had found to the newly returned Major Lorne. The scientist had practically pounced on him once they had returned; both _before_ he had seen Sheppard and _after_ he had figured the colonel was just stunned. McKinley was standing behind his shoulder with Torren perched on her hip, allowing him the privilege of revealing what they had found out – not that she had had much choice. Lorne seemed distracted though and kept looking over at the other unconscious person they had dragged in. "So we know what we're dealing with and how to stop it, right?"

"Well yes and no. We know for sure it's the _Alcoloniavarium_, but we can't just do what the replicators did because…"

"He's waking up." Lorne's head snapped around at Beckett's announcement and McKay found himself finishing his sentence to an invisible audience. Lorne left him hanging as he immediately went to the lieutenant's side.

McKay threw a glance at McKinley over his shoulder and she shrugged. Obviously the major had more important things to do at that point than listen to McKay. He left McKinley with Torren and wandered over to where Dr. Nakahara was tending to Sheppard. "Is he alright?"

The Japanese doctor looked up at his legitimately concerned face and gave him a tight smile. "He took another knock to the head and he's broken a few ribs, but he'll be fine once we've sorted this out and we can get him to the infirmary. He might not wake up for a while; I'm not sure how well the stunner blast will mix with the head wound…"

"I told him he shouldn't have gone," McKay muttered irritably. He dragged his eyes away from his friend who was looking way too pale and focused on being annoyed at him instead. Across the room the soldiers who had returned with Sheppard and Lorne were handing out TAC vests and wraith stunners to those that could use them. It reminded him of their first year during the siege where absolutely everyone had been armed to help defend the city. It wasn't a pleasant memory.

His reverie was interrupted by Beckett appearing by his side with surprising stealth. "Lorne was to talk to you about the Lieutenant." McKay nodded and slipped away with a final glance at Sheppard, and then Beckett came and knelt beside Nakahara. "How's our patient doing?"

"No change," she reported a little more truthfully than she had been with McKay. Both she and Beckett were well aware of the possibility that his head wound was a lot worse than it already appeared on the surface. They had patched him up as best they could with what they had, but what they really needed was the infirmary and its scanner. From across the room they heard Torren give an irritable cry and McKinley flashed Nakahara a panicked look. "I should…"

"Alright lass, you go help the novice child-minder," he smiled warmly and she stood up and went. He checked the wrappings she had done out of habit rather than a distrust in her ability. He was just checking the stitches along the hairline when Sheppard suddenly flinched, his eyes flying open. He seemed to regret the action instantly and squeezed them shut again. Beckett placed a hand on his shoulder. "Easy son."

"Carson…?" Sheppard blinked around them looking very confused. He took note of their location and tried to sit up. Again, the action proved to not be the wisest and laid back down with an annoyed look. "What happened?"

"What do you remember?"

"I don't…Teyla? Where's Torren?" This time he succeeded at pushing himself onto his elbows though it was obvious the movement was not comfortable.

Beckett attempted to push him back down as he explained, but the colonel was nothing if not stubborn. "He's fine; he's just over there with Dr. Nakahara. You really should stay lying down son…"

Sheppard pulled himself completely upright and propped his back against the nearby wall, earning himself a disapproving glare from the Scotsman. "The raid…did everyone get back?"

"Yes, you were the only one hurt. Apparently you managed to pick a fight with Ronon," Beckett's glare melted into a half smile. "I'm thinking you were lucky."

Their conversation was interrupted by McKay's return. The astrophysicist quickly hid his relief at seeing John awake with a smug yet irritated expression. "I told you so."

John blinked, but managed to hide the fresh blank spot in his memory by changing the subject. "You got a plan on how to fix this yet?"

McKay smirked. "Of course I do. Did you doubt me? I just thought I'd wait for Lorne so that I don't have to repeat myself. He's with the Lieutenant at the moment." They waited a few minutes and then Lorne came over and joined them, a strange look on his face. Sheppard decided to wait until after the disaster was averted to talk to him.

"You said you knew something?" Lorne asked as soon as he was within the group. He nodded at Sheppard to acknowledge his freshly conscious condition, and then turned back to McKay. "About the alco-something-or-other?"

McKay smiled broadly. "_Alcoloniavarium_, major. It's a nano-culture that the Ancients found. It escaped on them too and infected the whole city. If it wasn't for a bunch of replicators coming through the gate history would have played out a lot differently. They fixed the problem by emitting an energy pulse at a similar frequency to a stunner blast that dislodged the nano-particles from the Ancients and then used the original capturing device to re-contain them."

"So we do the same thing then?" Beckett asked.

"We can't," McKay replied with an irritated huff. "The device that captures them was part of the nanoscope they were also using to study them. The whole lot was in the lab that exploded a few hours ago. And also, we're not replicators – we can't just emit an energy pulse with a simple thought."

"So what? We can't do anything?" Lorne questioned, his tone growing impatient.

"I didn't say that," McKay held both hands up like he did when he was about to reveal a brilliant idea that no one else would honestly understand. "I have an idea. I'm going to need a lab with access to the city mainframe and a whole bunch of tablet PCs…Zelenka has a lab in Zeta tower that should do the job…"

"One problem, doc." Lorne interrupted. "The second we step out of here we're gonna appear on the city sensors. They'll be on us in minutes. Isn't there a lab within the blind section of the East Pier you could use?"

"Sir!" Came a whispered shout from the other side of the room. Lieutenant O'Brien held up a handheld life-signs detector that she had swiped during the raid. "I just picked up at least twenty life signs outside the blind area. They're heading this way!"

Sheppard had climbed to his feet unaided while their attention had been caught by the Lieutenant. Beckett didn't look pleased, and McKay could feel a bad idea coming. "I've got an idea."

* * *

><p><strong>12.35pm – Central TowerStargate Operations **

"Eye spy, with my little eye, something beginning with…'S'."

'Amelia' rolled her eyes at the one designated as 'Chuck'. He was leaned back in his chair, arms folded behind his head in a casual manner that he had learned from his host. He shrugged at her expression. "It's a game I found in my host's memory. Apparently the humans play it when they have nothing better to do. I simply pick an object in the room and tell you the letter it begins with, and you have to guess what the object is so…Eye spy , with my little eye, something beginning with 'S'."

"I am not playing this game. We _do_ have things to do; the Voice told us to co-ordinate the search. _You_ should be watching the sensors monitor, not playing stupid games." 'Amelia' scolded, though her eyes were subtly scanning the room for the elusive item beginning with 'S'. She glanced across at the glass office to see the Voice sitting at the desk completely unaware of 'Chuck's slacking.

"Or _maybe_ you just can't figure it out…" 'Chuck' goaded, although he did turn his chair slightly so that he returned to his assigned vigil. The screen hadn't changed since the last time he had looked, and he doubted the uninfected would show themselves again now that they had resupplied and found a good hiding place.

'Amelia' hesitated; double checked on the Voice, and then caved. "Is it 'stool'?"

"Nope."

"'Soldier'? 'Sandwich'? 'Screen'?"

'Chuck's grin grew wide at every wrong guess. The pair of them were very close to almost complete assimilation, the humanity of their hosts almost completely integrated into their own. It wouldn't be more than a few hours before they could erase the original consciousness and assume complete control. "Give up?" He raised his eyebrows as he glanced over his shoulder at her. "Okay, I'll tell you. It's 'Stargate'."

"But that's not in this room; it's in the gate room!" 'Amelia rebuked a little loudly. She threw another glance at the glass office but hadn't drawn her superior's attention.

'Chuck' smirked. "Yes, but I can see it from here. I win, my turn again. Eye spy…"

"You cheated!"

A loud rumble sounded from the gate room below as the chevrons around the ring began to light up in reverse. 'Amelia' leapt back into professionalism and typed at the laptop attached to the console before her. "Unscheduled off world activation." She said automatically, turning to another screen to check for an IDC. The gate shield was still raised preventing anyone coming through so the Voice allowed her to deal with whoever it was.

"Who is it?" 'Chuck' asked, looking eager for an excuse to do something other than stare at a screen of dots.

"Receiving IDC," 'Amelia' intoned as the computer beeped beneath her fingers. "It's an Athosian."

"What's an 'Athosian'?"

"_Hello? Atlantis? This is Kanaan calling from New Athos, can anyone hear me?"_

'Chuck' and 'Amelia' shared a look, both of them completely bewildered by the transmission. Their memory downloads were incomplete; a gap in which apparently included these _Athosians_. "Do I answer?" 'Amelia' asked, receiving an unhelpful shrug from 'Chuck'. Kanaan called again, worry lining his voice. She cleared her throat uncertainly, and then took the plunge. "This is Atlantis; we read you loud and clear."

"_Thank the Ancestors!" _Kanaan's relief was audible even over the radio. _"For a moment I thought…never mind. I was just calling to ask for Teyla. She and Torren were meant to have arrived a while ago…Can I speak with her?"_

"Erm…" 'Amelia' received no help from 'Chuck' who was once again leaning back in his chair watching her struggle. "Teyla is…Teyla is a little tied up right now…"

"_Oh."_ Kanaan sounded a little hurt by her reply. _"Can I ask what she is 'tied up' with?"_

"Erm…a meeting," she said a little too fast. "Er…Woolsey called a meeting unexpectedly, she must have forgotten to call to let you know…once they're finished I'll have her call you….'Kay?"

There came a pause over the line, and when Kanaan eventually replied he didn't sound convinced. _"You have not lowered the shield. Can I not come through and wait for Teyla to be finished in Atlantis?"_

"No."

"_Why?"_

"Because…because…because gate travel has been suspended while…Zelenka…runs some tests." 'Amelia' pulled the story out of her ass and it was obvious, but it wasn't like this _Kanaan_ of the _Athosians_ could do anything while he was on another planet and the gate shield was raised. "We'll let you know when she's done and the suspension has been lifted. Bye now."

"_What? No! Wa…"_

The Stargate shutdown with another mechanical whir and 'Amelia' blew out a breath in relief. 'Chuck' had a hand over his mouth as he tried not to laugh. "Shut up."

"Didn't say a word."

Sudden movement caught 'Amelia's eye and she turned to look in the direction of the glass office. The Voice had suddenly jumped to his feet, a smile on his face. As he strode across the bridge between the office and the control room the pair of them returned to proper professionalism; sitting up straighter in their chairs and giving their screen the attention they warranted. They looked up as the Voice entered as if they had been unaware of his approach.

"We've found them."

* * *

><p><strong>I will admit that I had to finish this chap this morning as I was falling asleep sitting upright even with three Red Bulls in my system – gives you wings my ass. I will make every effort to update quicker next chap! Sorry again!<strong>

**Let me know what you think :D**


	7. Broken and Blind

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

Thanks to BSBIlseD, JoeyLuv, BMick, Questfan, shepsgirl72, sheppardlover928, robvb2000 and wisconsinrocks for reviewing! Thanks for being so understanding about my tardy update and to Questfan, I might just take you up on that crate of Red Bull! :P

As always thanks also go to everyone who has read, alerted, favourited and/or also reviewed this fic so far – you are all truly fantastic!

At the end of last chap we officially hit the halfway point of this fic – I have planned for it to be 12 chapters long including a two-part epilogue that will hopefully stop me from rushing the end like I _always_ do lol…

But anyway...Enjoy!

* * *

><p><strong>Chapter Seven -:- Broken and Blind<strong>

**12.45pm – East Pier/Level 12 – Section Foxtrot **

"And where the hell are _we_ going?"

"We're gonna pull the ZPM; blind the sensors everywhere," Sheppard repeated as he ran the length of the corridor; McKay just about keeping pace behind him. His head and ribs hurt like hell, Beckett's patch job barely holding him together under the strain of the exercise. His breathing was heavier than usual and his head was pounding, but other than that he was doing a pretty good job of looking like he hadn't just been blown up that morning.

"That old trick?"

"Hey, if it ain't broke, don't fix it," Sheppard managed to quip back. They took a tight turn, purposely passing the transporter on that level in favour of another one – if anyone was watching, which was a pretty safe bet, he didn't want them to figure out where they were going.

"It's getting old, just so you know," Rodney retorted, his face reddening under the exertion of the full out run. "And it won't work – I pulled the ZedPM this morning to run power diagnostics – remember?"

John threw him a look over his shoulder and altered the route he had planned in his head. "So we're on back-up generators? Even better. We'll just pull the one for the central tower then."

"Oh, you mean the one 3 floors below Stargate operations and the nexus of Atlantis Zombieland?" Rodney snorted, annoyed by both the pace and Sheppard's devil-may-care attitude. "Great plan, Colonel. May I remind you that I am a fundamental part of the ultimate plan to fix this B-movie disaster and if you get me killed with yet another of your fabulous plans the entire city is screwed?"

"And can I remind you that we cannot do your plan until we've finished mine?" John threw back at him. He heard the astrophysicist huff but didn't receive a reply. Score one to Sheppard.

They took another corridor and a couple of flights of stairs before John relented and used a transporter. Part of him feared that if he stopped, even for the few seconds the teleporter closet took, he wouldn't be able to start up again. The reason he had chosen Rodney to come with him, other than the automatic 'McKay, you're with me', was that the scientist was the only one who would be panting worse than him from the run. If he had taken Lorne, which was probably the wiser choice, the Major would have been able to run laps round him. Besides, he was trusting Lorne to keep Torren safe – not a task he delegated lightly.

McKay was doubled over when the doors opened to the Gamma tower, his breath coming out in wheezes. He still managed to gasp out "What about the others?"

"If they keep moving until we cut the power, they should be fine," John replied, just about managing to regain the pace he'd set. Once the alert had been sounded that they had been found, he had ordered everyone to split up and keep moving before rendezvousing at the lab in Zeta tower Rodney had picked as their new headquarters. It had been a rush to get everyone out of the storage area – a bunch of zombie marines led by a trigger happy Ronon had arrived stunners-blazing just as Sheppard and McKay had left.

"Not them, I meant…when we left…I thought I saw…" it was rare for the fast-talking astrophysicist to struggle over his words. "I think I saw Carson get stunned…we left him behind…"

"He wasn't the only one," John admitted. He had seen what had happened but knew that starting a fire fight to free their stunned friends wouldn't have helped in the long run. He had shoved Rodney onwards hoping that the scientist hadn't seen. John had made the decision to leave them behind – he hoped to God it had been the right one. "A few scientists got caught too."

"They'll be alright…right?" Rodney asked, only allowing the emotion to come through in his voice because he was talking to John.

"Sure, they only got stunned. They'll just get taken back to the brig and we'll break them out later as soon as we're done with your plan," John reassured, though he didn't voice his own concerns. While he was glad that the zombies weren't shooting them on sight, it had led him to wonder what they were being captured for. He could tell Rodney was probably thinking along the same lines, but they both let the subject drop.

They travelled down a few levels and made another roundabout transporter ride back to the east side of the city before finally making the final stop in the tower. By the time they reached the corridor round the corner from the generator room, John knew he was in bad shape. The world kept moving after he had stopped and he could barely keep his aim steady long enough to stun the two guards outside. Rodney shot him a worried look when he staggered slightly as they made the short walk to the door, but he sensibly kept his concerns to himself.

The merry chase around the city had taken a lot out of the pair of them, but it had been necessary to throw their tracker off. If the other ATAs were doing as they were told whoever was watching them was probably going mental trying to figure out what they were doing. That confusion would buy them the time they needed…hopefully.

Sheppard entered the generator room with his stunner raised, leaving McKay at the door to watch his six. As he walked up to the generator and automatically began disabling it he came to the conclusion that Rodney was right and he had done this too many times. Without even thinking about it he pulled the key-like component off so that the generator couldn't be turned back on. Instantly the central tower was thrown into darkness. He tucked the piece into his newly acquired TAC vest and gave his walkie two clicks. That was the signal that the others were safe to head towards the rendezvous. He then stood up "What did I tell you, if it ain't broke, don't fix it."

"Um…John…"

"Oh crap."

* * *

><p><strong>13.15pm – Sigma TowerHolding Cell Zulu2-C**

Life in the Pegasus galaxy was always interesting and led to one witnessing many brilliant moments that could simply never be witnessed anywhere else. It also had its downsides though – if you lived there long enough and you got very accustomed to being stunned and waking up in a holding cell.

Beckett pondered whether or not the former outweighed the latter as the feeling began to return to his extremities. He quickly pushed the thought aside though as he decided that focusing on his current predicament was probably more important. He managed to push himself upright and then propped himself against the corner pillar of the cell. The first thing he noticed once the world had stopped spinning was that he wasn't alone. Around him in various states of unconsciousness were four scientists in blue. He hoped that they were the only ones and that they had been enough of a distraction for the others to get away.

One of the scientists, an Italian named Arrighetti, gradually came to. He blinked at their new abode warily, and then gave a resigned shrug. He then seemed to notice Beckett for the first time. "Fancy meeting you here."

Beckett gave him a half-smile, glad for the attempt at humour. He'd rather his fellow captives were calm and cynical than hysterical; but then again the others had already been here and done this before – for them it was just a step backwards. After their previous breakout someone had wisely decided to post more than two guards at the door, although Beckett doubted that another attempt would be made. The ones who had hopefully escaped had bigger things to worry about.

Eventually the others woke up as well. The two women, Dr. Fletcher, an Irish botanist, and Dr. Sharma, an Indian chemist, both stood up and paced around the space to work the feeling back into their legs. Dr. Arrighetti and Dr. Barker were lying flat on the benches counting the ceiling tiles overhead. There wasn't exactly much else by way of entertainment.

They were left stewing like that for ten minutes before the guards outside their cell suddenly stood up a lot straighter. An entourage of familiar people entered the room like an honour parade and took places around the edge of the cell. Beckett and the others climbed to their feet and converged together in the centre, their attention focusing on those at the back of the procession. Richard Woolsey stood in the middle, the menacing presence of Ronon at his left shoulder and Dr. Keller's emotionless stare to his right.

"You and the other Uninfected have proven to be more than just a nuisance to us," Woolsey announced. Every set of infected eyes was focused on him, all of them hanging on his every word. Obviously he was the one charge – maybe he was the voice everyone kept referring to? "Twenty-three minutes ago some of your kind managed to disable the power source to the central tower, effectively blinding us of their location. A logical move – but there are other ways to find them."

"We won't tell you a damn thing so don't even bother," Carson interrupted. Two years in Michael's captivity had hardened him somewhat and he decided to be bold. The other captives were looking to him as the most experienced in these kinds of situations, he was even the only one there that had been off-world.

"And I hadn't even asked you yet," Woolsey smirked. He then turned to Keller "They are intelligent, aren't they?"

"Yes. That is why the assimilation process is taking so long." Keller replied robotically, contrasting greatly to the far more human persona of Woolsey. Carson watched the interaction, picking up on the phrasing. It made sense that the alco-whatever-Rodney-had-called-it-varium would be a sentient species that learned from its host – the 'assimilation process'. It was apparent that it was occurring at varying rates; but what happened once the process was complete?

"No matter, it will be worth it," Woolsey replied. He then clapped his hands together to bring the conversation back to his original point. "Now, there are twenty-one dangerous unknown variables running around in my city – plus a baby – and I would very much like to know where they are and what they are planning."

"Like I said, we're not talking."

"And I had so hoped to do this in a civilised manner," Woolsey sighed. He nodded at Ronon.

The big Satedan was grinning as the door to the cell was opened and the force shield dropped. For every step into the cell he took Beckett and the others took a step back. The door was then closed behind him, effectively sealing them in with the dangerous possessed man. He drew a knife from his dreadlocks.

"Now then. I asked you a question. Would anyone like to volunteer an answer?"

Beckett's eyes didn't leave Ronon's blade, but he could hear the smug smile in Woolsey's voice. The threat was clear, and it wasn't empty. He could feel the fear and tension pouring off the others behind him; there was no way they would be able to stay quiet. Again, it fell to him. "We don't know anything."

With barely a flicker of movement Ronon grabbed Fletcher and spun her round to face them as he held her against him. The knife bit into her throat. The slightest whimper and she would cut it herself. She couldn't even breathe.

Surprisingly, Arrighetti took a step forwards, throwing up his hands "Wait! No! We don't know anything!"

"It's true!" Barker added, and Sharma gave a firm nod. Beckett felt a moment of pride. He had been so sure that the scientists would have caved but obviously he had underestimated them. He still doubted their ability to lie convincingly under pressure though, so he took over again.

"We didn't have time to discuss a plan," he half-lied. He laced truth into his answer to keep it credible. "The soldiers had not long returned from the raid on the weapons cache when you caught up with us. We simply ran – there wasn't a destination in mind. We really don't know the answer to your questions."

A tense silence fell following his words. Ronon still pressed the knife against Fletcher's throat and the poor botanist had her eyes squeezed tightly shut as she focused on not moving a muscle. Beckett watched Woolsey as he considered his response. The odd grin that grew across the man's face was not comforting.

"I don't believe you."

Ronon moved to complete the cut he had already started.

"But…"

Reluctantly, he loosened his grip. Fletcher sucked in a deep breath.

"I do, however, believe that you will stick to your story regardless of what I allow Ronon here to do. I fear he would kill all but one of you before you spoke the truth and I have a far better use for you in mind."

The grin grew Cheshire-cat wide. "Jennifer, commence the test."

* * *

><p><strong>12.40pm – Omega TowerLaboratory Romeo13-J **

'Teyla sat cross-legged on a table top in a meditative trance she had acquired from her host. Nearly an hour had passed since her host had had her moment of clarity and locked the pair of them in the lab, and it had been an hour she had spent wisely. She was learning, and the more she learned the stronger she became.

She couldn't even hear her host's protests anymore. Soon, its consciousness could be completely erased.

A smile tugged at her stolen lips at the very thought. It wouldn't be long before the challenge she had found herself would be conquered. During her assimilation she had discovered what had made her host so different – she shared common DNA with the race known as the Wraith. Their telepathic hive-like network, similar to the Collective's own, had led to them having naturally stronger minds. It meant that her host had had the power to fight back – unlike every other weak-minded human in the city.

It didn't matter anymore though. Her host had exhausted itself when it had briefly regained control earlier, making its constant struggles little more than a minor annoyance. Once she was free she would receive no trouble from her host. She would finally be able to complete her task.

She would kill John Sheppard.

She was shaken from her thoughts by a scuffle outside the lab door. She cracked open her eyelids to give the sound a disapproving glare. With a thought she identified the person on the other side to also be of the Collective. The Voice had finally forgiven her and sent someone to release her. She gave him her thanks and promised that she wouldn't let him down again.

She waited on the table still, her irritation growing with each minute that passed. Eventually the door began to open with a reluctant whine. 'Teyla' sprung to her feet and was by the widening gap before the person on the other side had got the door completely open. "About time."

"Omlouvám," the opener of the door apologised. "Musel jsem přesměrovat příkaz adresáře tak, aby provozní krystaly by spojil pouze s jednou stranou fungování ovládání dveří…"

"'Zelenka', is it?" 'Teyla' interrupted. The small Czech man nodded. "I cannot understand a word you are saying as you are the _only_ one of us who has that has learned that particular language, so if you wouldn't mind switching back to the default tongue?"

"Oh, ano, máte pravdu," 'Zelenka' agreed. "I was just saying that I had to reroute the command…"

"That's great," she stopped him again, unceremoniously shoving him to one side so that she could walk around him. "But I don't really care."

"Počkat! Where are you going?" he called after her, but she ignored him. She had better places to be and a more important person to see.

Once out of the corridor and away from the short scientist, she cocked her head to one side to connect to 'Chuck' in the control room. She was met with confusion as the technician struggled to comprehend the movements of the Uninfected life signs as they ran rampant throughout the city. He rudely cut her off, but she had all the information she needed.

In the last hour she had learned a lot about Lt. Col. John Sheppard. She knew the way he thought, she was well versed in how he fought and she had relived some of the stunts he had pulled in the past.

She knew exactly where he was.

* * *

><p><strong>12.40pm – New Athos Settlement <strong>

"_Bye now."_

"What? No! Wait!" Kanaan shouted at the communication device. Behind him the wormhole shut down with a whine and the radio in his hand went dead. He felt the small hope he had kindled from the initial conversation diminish back into the cold dread that had settled in his stomach a few hours earlier. He had known something was wrong even before Teyla had been late, her absence had simply confirmed it.

He turned to the tall man standing behind him, and Halling gave his shoulder a reassuring squeeze. "We must have faith that the Ancestors will keep their city and its occupants safe."

"Something is terribly wrong, Halling, I _know_ it," he replied, unable to draw on the comfort the gesture offered. Kanaan had always felt a strong connection with Teyla, to the point where it was as if he could read her mind. She had once explained to him that the gift that they shared meant that in a way he could. On an instinctual level he had always felt Teyla's presence – but now he could barely feel a thing. "Teyla…Torren…they are in trouble…"

Again, Halling tried to reassure him, but his words felt more like giving up. "There is nothing we can do while the Earth people keep the shield raised. Trust the Ancestors, Kanaan, they will keep them safe."

"I cannot just stand here and wait for some higher power to save them!" Kanaan practically shouted shrugging Halling's hand off his shoulder. Thankfully, the taller man didn't take offense from the outburst and tried to calm him with logic instead.

"What would you have us do instead? We cannot travel through the ring; we have no ship to fly there. We have no way to contact the Earth ships and call for help. Kanaan, I am sorry, I truly am, but there is nothing we can do."

Kanaan closed his eyes in defeat, knowing the truth of Halling's words. He then turned his face to the sky.

"Ancestors; please, please keep my love and my child safe."

* * *

><p><strong>12.40pm – East PierStorage Area Foxtrot5-C **

"Sir, I'm not sure…"

"There's no time Major! Now Move!"

Lorne did as he was told; both the tone of his CO's voice and the use of his rank telling him that there was no room to argue. He quickly turned his focus to the task at hand and grabbed a hold of Nakahara's arm. The Japanese doctor was clutching Torren protectively and he pushed her ahead of him as they headed out of the storage area's auxiliary door. Ahead of her was Captain Riley and next to her was McKinley. Together the five of them began the mad dash.

Behind him he could hear stunner blasts echoing around the space they had just vacated along with a few surprised grunts and fearful cries. Some of the ATAs must have gotten caught, Lorne realised, the thought piling guilt onto his already laden conscience. He had always believed that you never leave a man behind – who knew how many he had just abandoned?

He buried the emotion he had been fighting against all day and concentrated on their current situation. Sheppard and McKay were heading off to cut the power and blind the Collective, but while they were still visible the rest of the ATA's had to keep moving. It was both to avoid getting captured and to confuse the hell out of anyone who was tracking them. It was a good plan in theory, but Lorne knew that most of the people dashing around were scientists – not exactly the most physically able – could they keep running for as long as it took to cut the power?

As if to prove his point ahead of him Nakahara stumbled, already tiring from carrying Torren. McKinley saw and without slowing their pace took the baby from her. Lorne had been trusted with Torren's care, hence why he had chosen for both he and Riley to escort the two women and the baby. He needed the Captain on point while he covered their six – they could not get caught.

They moved in silence, Riley plotting their random route that would eventually lead them to the Zeta tower once the power was cut. Torren was passed between McKinley and Nakahara a few times to allow them to maintain their pace.

It was nearly ten minutes after they had started their run that finally the two clicks sounded from the walkie on his TAC vest. Riley heard her own and quickly led them towards a transporter. Once inside they were teleported in a flash of white light to the Zeta tower.

The lab that would be there new home was huge. It was filled with desks, chairs, computers and dry-erase boards along with some assorted Ancient tech hooked up to various machines. But that wasn't what caught Lorne's attention once they stepped across the threshold. The far wall wasn't a wall but a huge floor to ceiling window offering a panorama view of the city. Atlantis really was beautiful.

As they waited for the others to arrive Lorne and Riley took sentry positions by the door while Nakahara and McKinley took a much needed rest. Torren was still quite happy, not understanding what all the excitement was about but enjoying it nonetheless. From the bag of tricks Sheppard had thought to pack he had found himself an Earth-toy to entertain himself with and he sat on a desktop contently. He really was a resilient child considering all he had been through since his birth on a hive ship – and he wasn't even a year old yet.

The others came in dribs and drabs, all of the blue-uniformed scientists looking incredibly grateful that they could finally rest. They also appeared incredibly excited by the presence of technology and many of them found themselves a computer to play with.

Lorne watched the ensemble of people he had been entrusted with the safety of with a hint of pride. He wasn't sure if it was a testament to the people of Atlantis expedition or the randomness of the Pegasus galaxy that everyone there had kept it together under the pressure of a day he would rather forget. If he were honest they were pulling through far better than he was. Every time he stood idle, and sometimes even when he should've been concentrating on a task, he found his thoughts sinking further and further into the pit of guilt he had dug himself. He knew he would never be the same once this day was over.

"What now?" Captain Riley turned to him once most of the original headcount had been accounted for. There were still people missing – Sheppard and McKay hadn't returned, and Beckett and a handful of scientists were still absent – but nearly ten minutes had passed since the power was cut, it was time to move on.

"We get everyone back to normal," Lorne replied. He then turned to McKinley. "McKay said he had an idea, you got any idea what it was?"

McKinley hesitated. "Well, no, I don't know what the _actual_ plan was, but I know what he knew that led to him coming up with it." Lorne raised his eyebrows at her, which she took as her cue to explain. "The replicators defeated the _Alcoloniavarium_ last time by emitting a city-wide pulse of energy – similar to that of a stunner – and then using the original containment device to collect the nanoparticles up and seal them away in a dormant state."

"Yeah, I know that," Lorne replied. "But we can't do that because of a whole bunch of reasons. What are we going to do instead?"

McKinley shrugged.

"Well that's just great," he sighed, annoyed at both his CO and himself for sending the one person who knew how to fix the problem off to the central tower. What part of that had been a good plan? "Where the hell are they?"

* * *

><p><strong>A slightly shorter chapter, but a quicker update than last time :P <strong>

**Let me know what you think!**


	8. Explanations and Experiments

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

Super Duper thanks to my wonderful reviewers and readers – by now you all know who you are (or at least, I _hope_ you do lol) and how totally awesome you all are, so I'm not going to fill my word count with names and thanks…although I technically just did…nevermind!

Now to find out what made Sheppard say 'Oh crap' last chap :P

Enjoy!

* * *

><p><strong>Chapter Eight -:- Explanations and Experiments<strong>

**12.50pm – Central Tower/Laboratory Delta29-B **

"The excavation is complete," 'Keller' informed the Voice in a still robotic monotone. She hadn't had time to assimilate as much as everyone else as she had been in charge of co-ordinating the preservation of what was left of their Origin. She offered him her tablet PC "We have completed several tests and confirmed that the device is no longer functional. It is completely beyond repair."

"Good. They won't be able to use it against us this time," The Voice smiled, ignoring the computer – it didn't understand the diagrams and data anyway. "Have you been able to retrieve any live cells?"

"Negative," 'Keller' replied. She took back the computer and then laid it down on a cleared surface. She clicked her fingers at a passing scientist who eagerly showed her the tray he was carrying. She took a small glass tube from the tray and held it up to the Voice. "We have, however, found particles that we _believe_ are only dormant and could be _potentially_ woken by interaction with a host."

The Voice morphed its host's face into a vile grin that had no effect on the robotic doctor. "That's excellent."

'Keller' furrowed her eyebrows in confusion. "But there are no more viable hosts within this city. Without one the cells will simply remain dormant or expire from the damage they received in the explosion."

"Ah, but there _are_ hosts still here in Atlantis – the Uninfected," The Voice retorted as if the answer was obvious. It took the tube from her and held it up to the emergency light that barely illuminated the room. Inside was a tiny shard of glass; and somewhere on that shard was a nano-particle of the Collective, invisible to the naked eye. It was a kindred; sleeping as it waited for them to find it a new host to assimilate.

It was as it was intently studying the shard that the power to the Central tower was cut. A mechanical whine echoed throughout the structure, lights and computers fluttering out of life from top to bottom. Suddenly they were delved into complete darkness – even the emergency lights flickered out for a moment. When they came back on, the Voice's face was twisted into a mask of anger and annoyance. It thrust the test tube back into 'Keller's grip and left the room.

Once outside in the corridor it telepathically demanded an update. The one designated as 'Chuck' in the control room was quick to proffer apologies as he explained that he hadn't been able to properly track the Uninfected life signs before two of them had succeeded in taking out the generator that powered that tower and the two neighbouring it. They were now completely blind; the sensors having been rendered dead without power. They had no idea where the Uninfected were…or what they could be doing.

"Damn it," the Voice hissed, the curse springing from its host's vocabulary. First the raid on their hideout resulted in the capture of barely any of the damned pests, and now they were running free around its city.

They would pay.

"How many cells did you manage to collect?" The Voice asked over its shoulder. 'Keller' appeared by its side with the tray she had taken from the scientist.

"Three that are suspected to be most likely dormant and five more that are confirmed expired. We are still searching for more."

Not as many as it had hoped. "That will have to do. Summon 'Ronon' to the holding cell. Let's go and visit our guests."

* * *

><p><strong>12.50pm – Central TowerGenerator Room97-F **

"Um…John…"

Sheppard turned around at the nervous tone of Rodney's voice to find the scientist firmly wedged in a stranglehold, a 9mm pistol pressed firmly to his right temple. The one holding him was a very determined and cold-hearted-looking Teyla. He drew his stunner but knew he couldn't use it. "Oh crap."

A smile tugged at her lips, but it didn't belong to her, the expression twisting her beautiful features into an alien mask. In the emergency lighting of the room they were all thrown into a low red glow, the effect magnifying the intent on her face. When she spoke she had adopted Teyla's cadence, but the venom in her tone reiterated just how not-herself she was. "Repair the generator, or I will blow a hole in Dr. McKay's head."

"You wouldn't," John tried to talk his way out. Yes, he was armed with a stunner and could simply stun Rodney and make her drop his dead-weight; but then he'd have to carry Rodney all the way to the Zeta tower. There was no way he could do that in his current condition, especially with the transporters in that tower out as well. "Teyla would stop you like she did last time."

Her smile turned into a smirk. "She cannot. She is too weak now; barely a whisper in my mind. Do not doubt my strength and ability, John Sheppard. I will kill Dr. McKay. Repair the generator."

Rodney remained silent during the exchange; quite a feat considering he _was_ Rodney McKay, but now he spoke up, saving John from having to come up with a bluff. "Well he _can't _fix the generator, can he? Colonel Trigger-happy here has damaged it beyond even _my_ extensive capability to fix."

"So you have outgrown your usefulness then?" Teyla replied, pushing the barrel of the gun hard enough to leave an imprint on his forehead.

"Wait!"

"What are you talking about? I am _Rodney McKay_ – I'm useful in tons of ways!" Rodney instantly began to babble over John's protest. "I know more than all your mind-controlled zombie scientists put together – I am a very important, useful, and intelligent person!"

Teyla raised her eyebrows at him "So it would be a shame to paint the walls with your rather substantial brain matter then?" Rodney held his tongue. She then looked over at John. "I guess it is safe to assume that he is as important to you as he claims to be for us? Surely he has come up with some solution for your, what did he call it? Your 'zombie' problem? That leads me to conclude that he is rather dangerous to us; and all threats to the Collective will be eradicated. Repair the generator and I might consider re-evaluating my assessment."

_Damn it._ John ran through his options, realising just how few and bad they all were. He could repair the generator in around ten seconds; but then the others would be visible and by now would all be in one place – easy to find and capture. And even then there was no guarantee that that would even save Rodney. Again, he considered stunning Rodney, but the fact that just remaining standing was proving a challenge for him confirmed that he really couldn't lug the scientist around and they wouldn't have time to wait for him to wake up. Talking their way out wasn't working. Lying was digging them a deeper hole. So what the hell was he going to do?

It was then that John began to string fragments of his scattered memory together. This was the third time that Teyla had found him – that he could remember. Every time she had found him she had tried to kill him, and every time she had failed. In the corridor on the way to the brig a few hours ago, even though it felt like months, she had reacted to him when everyone else had ignored him. Something about Teyla, or the thing possessing her, was obsessed with him. He almost laughed, but tamed it into a smirk instead. "You're pissed at me, aren't you?"

Rodney gave him a weird look, but Teyla just blinked, and John knew that he had hit the nail on the head.

"Because I got away?" he continued at her flabbergasted expression. "What? Did it put you in your boss's bad books because you kept failing? I hate to tell you this, but that's not my fault. The real Teyla could have kicked my ass back to the twentieth century without even breaking a sweat."

"Silence!" Teyla shifted slightly, taking the gun from Rodney's head and aiming it at him. McKay didn't know whether to look shocked, worried or relieved at the turn of events. He was still trapped, but his life wasn't being immediately threatened. "It _is_ your fault! The Voice _loved_ me! Ever since you got away he has treated me like a _failure_! It is not my fault that my host is a freak of nature!"

Obviously John had hit a nerve; a rather dangerous one considering the anger that wrapped her finger around the gun's trigger. But it had had the desired effect – her attention was entirely on him, her grip on Rodney loosening as she seemed to forget he was even there. He met McKay's eyes, telling him to be ready. He then tightened his grip on the stunner, waiting for the right moment.

But then her attitude changed. She suddenly stopped shouting, her voice settling into a threatening tone. "But that does not matter anymore. Soon she will be gone and you will be dead. Goodbye, John Sheppard."

"McKay!"

Everything happened in the same millisecond. At John's shout, Rodney managed to rip himself from Teyla's weakening grasp and throw himself to the ground. Teyla squeezed the trigger. John fired the stunner.

A few seconds passed before Rodney raised his head. Teyla had crumpled next to him, the literally smoking gun still loosely held in her hand. Panic raced through him as he pushed himself upright to scan the room. At the base of the generator stand was another dark heap that wasn't moving. "John!"

He skittered across the space between them and crouched by his side placing a tentative hand on his shoulder. In the near-darkness of the room he couldn't see properly. He held his breath without realising until Sheppard eventually opened his eyes. "John? Are you alright? Did she…?"

"N-no," he gasped out. His right arm was pressed tightly to his side as he tried to control his breathing. "Sh-she missed. Just jostled my ribs is all. Give me…a minute."

To avoid the bullet he had dived hard to the left as he had fired the stunner; the impact with the ground reminding him that he was in no shape to pull off such a move. The pain had been enough to black him out for a moment – but at least he hadn't gotten shot. That would have been the cherry on top of the cake of a very crap day.

Rodney was watching him, unsure what to do while he struggled to manage his pain. After a minute that felt like an hour for both of them, John eventually nodded. He pushed himself upright with his good arm, stifling the cries of agony into grunts, still adamant that he wasn't as badly hurt as he honestly was. Rodney scooted round to his left and gripped his arm without a word, helping him to his feet.

Once steady on his own two feet, he threw McKay a wry smile. "How many stairs do you reckon it is between here and the nearest working transporter?"

A look of horror spread across Rodney's face. "This was a terrible plan."

* * *

><p><strong>13.30pm – Sigma TowerHolding Cell Zulu2-C**

"Jennifer, commence the test."

Beckett felt his blood run cold. It was as if the temperature in the room had suddenly dropped ten degrees just at those few words. He glanced around at the others. Arrighetti was holding a very scared and pale looking Fletcher while the others stood frozen to the spot, much like Carson. He had wondered why they were being captured alive – and now he knew. They were human guinea pigs. "What test?"

Jennifer and Woolsey ignored him. She took a tube from a tray one of the zombie scientists was holding and began pouring various liquids in. She then took a syringe and filled it with the finished solution. She turned to Woolsey. "Who shall I inject?"

"What test?" Beckett asked again, more forcefully this time. He stepped in front of the others, warily keeping an eye on Ronon who was lurking dangerously nearby. The door opened again to allow Keller in.

"Inject them all." Woolsey ordered.

"But we only have 3 live…"

"Then use the dead ones as well." He interrupted. Keller nodded and stepped into the cell followed by a handful of marines. Outside the scientist was prepping four more syringes – one for each of them. Woolsey nodded at Arrighetti who was still gripping Fletcher protectively. "Begin with the hero."

Immediately Ronon divided the pair and held onto the Italian so tightly he couldn't even try to struggle. Beckett and the others moved forward to intercept, but were held back by the marines. Arrighetti had a resigned expression on his face as Keller came to stand before him. He threw Beckett a look before his attention was caught on the needle in her hand. She plunged the sharp point into his neck and shot the strange solution straight into his bloodstream.

"Well?" Woolsey demanded impatiently.

Keller studied Arrighetti's face, staring intently at his eyes. She shook her head. "If it works, the effect will not be immediate. Shall I continue?"

Woolsey nodded and the scientist entered with the other syringes. Ronon threw Arrighetti to the ground and grabbed the next one. Once again Keller injected the scientist, studied him or her, and then moved on to the next. Beckett was left until last.

Ronon effectively paralysed him in a hold, wrenching his head to one side to allow Jennifer access to his neck. As Carson stood helpless to the experiment inflicted upon him, his thoughts wandered to a Wraith that they had named Michael Kenmore. There was nothing like the taste of one's own medicine. He squeezed his eyes shut as the needle point was pressed into his flesh, the sound of the liquid being ejected sounding loud in his ear.

And then it was over, and he was thrown on the ground with the others. He rolled on impact with the concrete and pushed himself upright. "What have you done to us?"

Keller, Ronon and the marines left the enclosure and re-joined Woolsey outside. The cell door closed and the force field reactivated before Woolsey felt the need to answer.

"Do you know how we work, doctor?" he asked, stepping up to the bars. Carson climbed to his feet and stood opposite him. "All we do is land on the skin of a host and instantly we are tapped into the central nervous system and are given complete control. We are tiny, so small that you can't see us, but there we are, just sitting on the surface. Once we are there we begin to learn. We study our hosts, download everything there is to know about being them, and then we take over. We erase the consciousness that was there before and replace it with our own. To an outsider, it would appear as if no change has happened; we assimilate so completely."

It was like that film; Carson thought to himself. The one about the body snatchers. They don't just take over and possess their hosts: they replace them. The implications began running through Carson's mind – how long did the process take? How many people had they already lost? Was there even anyone left to save?

"But there is something different about you and the other Uninfected," Woolsey continued, irritation working its way into his voice. "For some reason we cannot latch onto you properly. We cannot access your nervous system. We cannot control you. This poses a problem and a threat to us; and all threats to the Collective will be eradicated. However – we have kindred with no home and no purpose, and you are the only potential hosts left in this city."

Realisation dawned on Carson's features as he figured out what had been in the syringe. He realised what was flowing in his bloodstream right now.

Woolsey grinned as he watched Carson's face. "We found a few cells of our culture that had survived the initial explosion but hadn't found hosts. We believe that by being injected directly into the bloodstream they may be able to assimilate that way. We will find out soon enough."

Carson suddenly felt very sick to his stomach, the pain in his abdomen making him double over and then collapse to his knees. His head pounded as the blood that rushed around his body was pumped by his too-fast heart. Sweat began to bead on his forehead as his body rejected the foreign particle. "Bloody hell!" he gasped out, just about refraining from curling into the foetal position.

"It appears to be a negative reaction."

Carson heard Keller tell Woolsey, but the entirety of his concentration was stolen by his need to throw up. He tried to fight the urge for a while, but eventually he just gave in and spilled his breakfast onto the cell floor. He coughed and spluttered and retched until there simply wasn't anything left to escape his stomach. He sagged onto his side next to the puddle, the smell making him feel worse.

After a few minutes the pain began to subside a little, although he still felt exhausted. He wiped at his mouth as he pushed himself back onto his hands and knees and then onto his feet. Carson glared at Woolsey with a hatred he hadn't known he was capable of. "Satisfied?" he managed to remark.

Woolsey was smiling; not quite the look Carson had been expecting. "Yes, I am."

Beckett furrowed his eyebrows in confusion, and then realised Woolsey was looking past him. He turned slightly to look at the others that had stayed behind him. Dharma was looking as pale and ill as he felt, while Fletcher and Arrighetti were still lying on the ground shaking violently. Barker, on the other hand, was standing upright and glassy-eyed, staring straight at Woolsey. "What does the Voice decree?"

The door to the cell was opened again, and Barker, now a member of the Collective, was allowed to leave and join his kindred. The door closed behind him and just the four of them were left behind. Carson stepped back up to the bars. "What about us?"

Woolsey shrugged, nodded at Keller, and then turned and left, the others following him but leaving her behind. "The cell injected into you and the other female were confirmed to be expired. Your bodies ejected the cell and allowed you to live. The other two were injected with dormant cells. Their bodies are rejecting the cells and they will eventually die along with our kindred. The experiment failed."

Keller looked disappointed at the failure, and then followed the previously departed out of the room. Carson turned around and shared a look with Dharma.

They were left to watch Fletcher and Arrighetti die.

* * *

><p><strong>13.05pm – Zeta TowerLaboratory Quebec89-X **

McKinley lay on the floor, her legs at a right angle to her body against a desk, a tablet PC propped on her stomach. It was what she did when she was put under pressure, elevating her legs in the vain attempt to get the blood flowing to her brain and make her think clearer and faster – it wasn't working.

She stabbed irritably at the computer's touch screen trying to force a brilliant idea like the one McKay had had, but had neglected to tell them. Despite the fact that she wasn't a scientist – not even a college education under her belt – she had been delegated the task of finding the magic solution. Apparently she was the closest thing to an expert that they had, simply because she was the one that had happened up the _Alcoloniavarium_ in the first place.

They couldn't have been more wrong. Her speciality was computers. She could do anything with them and understood them in such a way it was almost as if she spoke their language. It was her skill as a hacker that had landed her in the Pegasus galaxy in the first place. So now she turned to the one thing that had never let her down to get them out of this mess. She continued to study the entry that Ilya, a 10,000 year old replicator, had written.

The answer had to be in there. It _had_ to be.

Where the hell was McKay?

As if in answer to a prayer, there came a scuffle of activity from the door. Immediately McKinley rolled onto her feet, clutching the computer to her chest. She couldn't help the outburst that escaped her lips when she gratefully saw the two men who had arrived "What the hell took you so long?"

"Sorry, got lost," Colonel Sheppard quipped. He was standing by himself, but she could tell that he wouldn't remain that way for long. He found himself a seat once he had confirmed that Torren was safe. He looked exhausted and in pain, but he didn't stop. He turned to look at McKay who had sprawled himself on the floor. "So, what was your plan?"

Those who hadn't noticed their arrival were now staring expectantly at the astrophysicist along with everyone else at Sheppard's words. McKay reluctantly pulled himself upright and leant against a desk. "How many people have we got?"

"Twenty-one, plus Torren," Lorne replied. He was looking as relieved as McKinley felt now that the man with the plan was there.

"That'll have to do," Rodney replied. He clicked at McKinley in an expectant demand for her computer. She was tempted to make him actually ask – maybe even use the word 'please', but decided time was of the essence and that she could teach him manners later. "Right, everyone knows how the Collective was defeated last time, right? Well, we can't do that. One; we're not replicators, Two; the bait and trap the Ancients made is completely destroyed, and Three; I like to be original with my city/planet/galaxy saving plans."

Sheppard smirked, and then made a gesture that McKinley translated to mean 'get to the point'.

"So my alternative plan is simple," McKay drew the same meaning. "We are going to turn the city shield into an energy pulse by uploading a program into the individual emitters that will alter the shield's frequency to a level similar to that of a stunner. We will also reprogram the city's life support system to complete a rapid air cycle to suck up the nanoparticles. We will also need to adapt a containment vessel to hold the collective cells once they have been separated from their hosts and channelled through the air filtration system."

"What part of that was 'simple'?" Sheppard asked after a moment of silence from the entire room.

"Well, the programming for the shield emitters should be pretty simple," McKinley piped up, requisitioning another computer from a scientist's grip. She got to work straight away, remembering the last thing she had read in the database entry – they were on a time limit. "I could probably simplify it enough to make it almost a plug'n'play programme."

"That's great and all, but is no one else seeing a problem?" Lorne interjected. "If I'm understanding you right, we're going to need to activate the shield – doesn't that mean we need the control room…which is currently full of zombie personnel _and_ has no power?"

"You can activate the shield from the chair," Sheppard answered before McKay had even opened his mouth. "The chair room still has power and it shouldn't be as heavily guarded as the control room. You could probably turn it into auxiliary control for the entire city."

"Exactly, gold star for the Colonel," McKay retorted as he also began working on the tablet PC he had borrowed from McKinley. "We can update the life support system from the chair room as well, although we'll need to alter the air filtration system in the maintenance room. We should probably initiate a lockdown to restrict the movements of the zombies but allow those with the ATA gene to move around as well."

Lorne nodded, just about following, but then he furrowed his eyebrows again. "So let me get this straight – you want to turn the city shield into a massive stun weapon? Wouldn't that affect us too?"

McKay paused mid-type, and looked up at the Major. "I'm not entirely sure. Technically, it's not _actually_ a stun weapon – the energy pulse should be at a slightly different frequency that might potentially not affect us…but I can't say I've had time to run tests to check. We'll automate as many processes as we can so that the plan is carried out even if we are unconscious, though, so it should be fine."

"Well that's comforting," Lorne replied, sounding not at all comforted. He looked around the room, reassessing the head count and sorting people into groups. "So, who's doing what then? I want at least five soldiers with me when I take the chair room, and I'll probably need a scientist as well to do those update-things."

Sheppard noted Lorne assigning himself a role without his superior's permission; something he never would have done a few years ago. Under the circumstances, and the fact that _technically_ Sheppard wasn't even on duty, he decided to let it slide. "And there are ten shield emitters," he added. "We should split up whatever scientists are left and pair them with a soldier as protection."

"I'll need three underlings to work on the containment vessel while I customise the air filtration system," McKay tagged on the end, not looking up from his computer.

"We'll leave Nakahara here with Torren. Once the lockdown's initiated they should be completely safe," Sheppard continued, and received a nod from the medical doctor.

Lorne, on the other hand, didn't look too pleased. "Sir, with all due respect, shouldn't _you_ stay behind…?"

Obviously the Major had gotten tired of being overruled by his stubborn CO who kept putting himself on missions that in all honesty he probably shouldn't be doing. Sheppard decided to ignore the truth of Lorne's statement. "I've done the math, Major. McKay plus three scientists to the maintenance room; you plus one scientist plus five soldiers equals eleven. That leaves four soldiers, three scientists, a gate tech and myself to cover ten shield emitters. We pair them off and give them two emitters each, that just leaves me to fix the last two. Am I wrong, Major?"

Lorne didn't answer; probably a wise decision considering the determination on his CO's face.

McKay, however, had no reservations against arguing the point. "Yes, but there is a _reason_ we are sending scientists to the other emitters. Do you know how to reprogram them to the exact right frequency?"

Sheppard gestured at McKinley, her name once again escaping him. "Plug'n'play."

"I think it's a little more complicated than that…"

"Then make it simple."

"We don't have time for this!" McKinley surprised herself with her forceful interruption. While they were being productive she had no problem letting them talk things out; but now she was becoming increasingly aware of the minutes passing and their approaching deadline. "We are on a time limit here!"

"What do you mean?" Lorne asked, the confusion on his face mimicking everyone else's in the room.

McKinley found herself gesturing with her tablet PC. "I found out what the _Alcoloniavarium_ does. Their sole purpose is to learn, so they take over a host, download all of their thoughts and memories, and once they're done…once they're done they _erase_ the original consciousness and _replace_ it with their own."

"How long?"

"Well, it varies, but in the replicator's account she claimed that they returned to Atlantis within three hours and had it fixed within one. By which stage they had already lost a third of the population. It's been two hours and forty-eight minutes since the explosion." McKinley said as she checked her watch.

"The longer we stand here arguing, the more people we lose."

* * *

><p><strong>Dun, dun, duh! The ticking clock has finally been revealed to the people it actually matters to lol :P<strong>

**Sorry that this chap had a lot of talking – particularly towards the end – but it was necessary to establish the ridiculously complicated plan I managed to come up with to solve the problem. The good news is that the action starts next chapter!**

**Let me know what you think – and I'll see you next chap!**


	9. Seperation and Solutions

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

'Thank you' really doesn't cover how grateful I am to all of my super-fantastic-amazing reviewers and readers! I hope this next-day update is quick enough lol, though I warn you – you wont get another one tomorrow, Morrisons beckons :P

And to robvb2000, that's a good idea – I hadn't actually come up with a reason lol, but that totally makes sense :P I'm gonna use that!

And last but not least, I want you all to witness my little happy dance I am currently doing – This fic is now officially the LONGEST and has had the MOST REVIEWS I have EVER gotten…and it's not even finished yet! Thanks for making this possible – my muse probably would have gone on strike without you!

I'm done now (well…I'm still dancing, just so you know…) Enjoy!

* * *

><p><strong>Chapter Nine -:- Separation and Solutions<strong>

**13.35pm – Zeta Tower/Chair Room Yankee3-A **

Miranda McKinley was painfully aware that they had already passed the three-hour mark. As she cowered in the corridor around the corner from the chair room waiting for the all clear from Major Lorne, all she could think of was of the sheer number of people that were currently being erased from existence. Sure, they would be in time to save some of them – but who knew how many they had already lost?

She could hear the sounds of battle emanating from down the corridor. There came the concussive explosions of stunner blasts connecting with the walls, almost drowning out Lorne's orders to his band of marines. Thankfully, there had been no gunfire – apparently the Collective were still holding out hope of capturing them alive; but to what end? She didn't even want to think what was happening to Dr. Beckett and the others that had been captured earlier – were they too late to save them as well?

As she waited she clutched a tablet PC to her chest, the program needed to update the city's lockdown procedure already written and ready to be uploaded as soon as they had access to the chair room. McKinley had been the one selected to go with the soldiers because Dr. McKay had been silently impressed with her computer skills and felt she was the best one for the job. He didn't say that of course, just grunted and pointed at Lorne when the time had come for them to split up; but McKinley had read between the lines. And now here she was, practically the co-ordinator of the rescue attempt of the entire city.

It was hard to believe she had only been in the Pegasus galaxy two days. There was nothing like a trial-by-fire to prove her worth to the expedition.

Hours seemed to pass before Lorne finally called for her, but she checked her watch to find it had been less than five minutes. It had taken longer than expected to get everything ready for this epic of a plan – they had had to write and upload the shield emitter program onto five tablet PCs, as well as write the algorithm that would update the lockdown procedure and organise who would be going where. Thankfully it had only been a quick transporter ride down the building to get them to the chair room, and Lorne and his soldiers were efficient at tactical assaults.

With the coast clear she darted out of her hiding place and ran the length of the corridor and into the chair room. Under any other circumstances she would have stopped and stared at the set up in awe – how could that throne control some of the most dangerous weapons ever created? But she squashed her inner-tourist and went straight to a console. She found the slot for the Ancient tech adapter attached to her computer and plugged it in, wasting no time in beginning the upload.

As she silently urged the progress bar to move faster she was vaguely aware of Lorne and his men (and woman) dragging the stunned soldiers outside of the chair room doors so that they would be outside when they woke up. She couldn't imagine how disorientating it must be to wake up in a weird place with no memory of how you got there or what the hell had happened before hand. Explaining this day was going to be interesting.

"How we doing, doc?" Lorne asked once he had returned, appearing stealthily by her side. She didn't feel the need to correct him of the fact that she wasn't a doctor, it really wasn't the time.

"Almost done," she replied instead, her impatience growing at the slowness of the progress bar. She wished she had a computer with a faster processor; but they had been limited by the resources they had had available. Honestly, they were lucky that they had had any computers at all. Finally, the bar filled to 100% and the computer beeped contentedly. "Done! Activating citywide lockdown!"

The door to the chair room; along with every other door in the city, slammed closed and stayed locked that way. They would only open if someone with the ATA gene swiped the door control – she had updated the procedure that allowed those in hazmat suits to pass through the city during a quarantine to instead identify the gene. It meant that all the infected would be stuck, but McKay and his team and those heading towards the shield emitters would be able to move freely.

Suddenly; the walkies on their TAC vests hissed to life.

"_Oh, nice timing,"_ came McKay's sarcastic comment, and McKinley threw Lorne a look.

* * *

><p><strong>13.35pm – Omega TowerSection Juliet Level 64 **

"Are you sure we shouldn't have an escort too?"

McKay glared irritably at the scientist walking next to him. Dr. Marcus Giles, along with the other two he had picked to come with him, were looking very nervous. They stayed behind Rodney the whole time, their grips on the Wraith stunners he doubted they even knew how to use turning their knuckles white. It was then that he remembered that none of them had been cleared for off world duty due to their 'nervous dispositions'. He was going to have to pay more attention to personnel files. Maybe he should learn a few names.

"I mean, we're the only group that doesn't have any soldiers…I mean, _none_. What happens if _we_ run into a bunch of zombie marines?" Giles continued, and McKay felt his irritation rise.

He stopped suddenly mid step and spun to face them. They almost walked into him due to the abruptness of the manoeuvre. "Look, the reason we don't have an escort is because there wasn't any soldiers _left_. Would you rather we had left one of the others to wander around _alone_? There are _four_ of us – if we run into anyone, which I highly doubt, we can take care of ourselves! Understood?"

"Um…Dr. McKay…" another scientist, Caruso...or something, interrupted nervously. Rodney was instantly towering over the rather short man.

"What?"

Caruso pointed over Rodney's shoulder in the direction they were meant to be heading in. McKay knew he was about to eat his own words. "Oh, for God's sake."

Giles barrelled into the side of him as the first stunner blast hit the air where his head had been milliseconds before. They both hit the floor and struggled ungainly back onto their feet and into the cover of a recess in the corridor wall. A quick glance showed that Caruso and the last scientist, Eklund, had had the sense to do the same opposite. McKay fumbled to get his own stunner out of the holster on his thigh and then fired randomly around the edge of the protruding wall.

He then felt brave enough to take a peek outside of his relatively safe spot in order to actually take aim. What he saw almost made him laugh – in a mad, adrenaline and fear induced, spur of the moment kind of way. Leading the enemy that now bore down on them was none other than Dr. Radek Zelenka – and his army was a handful of blue-suited scientists who were about as adept at gun fighting as McKay was at knitting.

"Pro Kolektivní!" the Czech yelled over the din of the stunner fight.

McKay didn't think it could have been a weirder, or more ironic, set-up. There he was with his inexperienced platoon of 'nervous dispositions', battling against both his rival and friend with his own green team. What were the chances?

That didn't matter though as McKay realised that he had the upper hand. He had been on a gate team for five years, and not just any gate team; but the flagship gate team. He'd been in more fire fights than he cared to count, and, though he suspected Sheppard would beg to differ, he thought he was getting pretty good at holding his own. He had training and experience that Zelenka and his band of misfits couldn't even imagine. Rodney could totally kick his ass.

"Vzdejte se ty ubohá omluva pro astrofyzik!"

"I don't even know what you're saying you idiot!" McKay shot back, taking the Czech rambling as an insult.

The two groups exchanged a series of shots, most of which hit nothing but empty space, but a few hit home. McKay was pleased to see that he had already taken down half of Zelenka's team before he got off a lucky shot that took out Eklund. Soon, there was no one left but the Czech, who as such decided to make a kamikaze charge.

"Jako Hlas dekrety!"

He didn't get very far before Rodney got him with a single shot. He let out a jubilant shout "Hah! I told you so!"

Giles threw him a poisonous glare and joined Caruso by the unconscious Eklund's side. Rodney was feeling a little giddy as the adrenaline rush continued to run its course, but it quickly turned to annoyance when a siren suddenly sounded and a bulkhead slammed closed in the middle of the hallway; effectively separating them from Zelenka and his group. He activated his walkie with a click "Oh, nice timing!"

He didn't receive a reply. He turned to the others. "Come on, we'll find another way round."

* * *

><p><strong>13.45pm – Sigma TowerHolding Cell Zulu2-C **

Dread and powerlessness flooded Carson as he realised there truly was nothing he could do. He crouched between Dr. Fletcher and Dr. Arrighetti, able to offer little more than meagre comfort. Both of them were curled in on themselves, groaning in pain and occasionally thrashing as a spasm ran through their bodies. Carson couldn't even give them pain relief – all he could do was watch.

Dr. Dharma was crying silently as she sagged nearby, looking as helpless as Carson felt. He looked up at the prison door at the group of soldiers that were assembled as guards. His voice broke slightly as he angrily yelled in desperation. "Hey! We need some help in here! Hey!"

He didn't know what he was expecting, but he got nothing but silence in reply regardless. He met Dharma's gaze and communicated what they both knew but were frightened to say. There was nothing they could do. Fletcher and Arrighetti were going to die –and they were to watch.

Gradually, the spasms began to subside into violent shivers. They were pale and covered in cold sweat, their faces carved with deep lines of pain. From his place between them, Carson gripped both of their shoulders in an attempt to lend them strength. Maybe this was a good sign, he thought as he watched them calm slightly. "You're going to be okay."

"D-don't l-lie," Arrighetti replied, his teeth chattering around his words. Carson felt his own tears threaten to fall as he watched the Italian reach a hand over to Fletcher and grip hers tightly. "R-Ro-wan…"

Carson hadn't even known her first name, but he watched as Rowan Fletcher attempted to smile at the dying man lying next to her. "Y-yes?"

"I'm s-sorry I-I n-never t-told you th-this be-f-fore," his sentence was broken by the shivers that wracked his body. Carson looked away, realising what was happening and allowing them as close to privacy as he could give them. "B-but I l-love you…have, f-for a w-while now…sh-shame it t-took d-death f-for me t-to tell y-you…"

Tears joined the sweat that poured down Fletcher's face, a sob escaping between a forceful spasm. She managed a watery smile then, gripping Arrighetti's hand all the tighter. "I l-love y-you t-too…sh-shame it t-took death for m-me to t-tell y-you…"

Now Carson was crying freely, though his face was still turned away. He wished that there was something, anything, he could do. He wanted more than anything for the two people lying around him to live; to act on the feelings they had finally admitted to each other. His heart broke for them as he listened to them. He could hear Dharma sobbing nearby, just as upset as he was. He then felt a weak grip on his arm, and turned back to face Fletcher gazing up at him.

"C-Carson…c-can you d-do me a f-favour…?"

* * *

><p><strong>13.40pm – West PierSection X-Ray Level 4 **

"It's O'Brien, right?"

Harvey the gate tech tentatively asked his rather beautiful, female, military escort. She threw him a look over her shoulder, and then turned back to scanning the corridor ahead. "Lieutenant O'Brien of the United States Air Force," she replied formally.

"But, you have a first name, right?" Harvey continued, apparently oblivious to the cold shoulder she was giving him. There was a silence as they kept moving forward and then took a left, heading towards their first shield emitter. He held the tablet PC with the necessary program uploaded on it to his chest protectively.

"Caitlyn," she eventually replied.

Harvey smiled; pleased that he had made some progress. "That's a pretty name, suits you."

O'Brien didn't answer. She was of an Amazonian build; incredibly tall and muscular and yet still very feminine. She looked every bit a G.I. Jane in her uniform and TAC vest, her Wraith stunner held ready before her. Harvey was pretty sure he was falling in love. What were the chances of _him_, the gate tech that no one knew, being paired with this beauty? Surely, it was meant to be.

It was time for the big guns. "I'm glad I was paired with you, you really are beautiful – and you know what they say about beauty right? It protects against all evil. Well, with you I feel really safe."

O'Brien suddenly stopped, her body tensed. Harvey immediately back-pedalled. "What? Was it something I said? I didn't mean to…"

She spun round, stunner raised and aiming straight at him. Great, so he'd been paired with a gobsmackingly gorgeous psycho? Well, he'd had worse girlfriends. "Wait!"

She pulled the trigger, and Harvey squeezed his eyes shut expectantly. A second later, when he found himself still conscious, he opened them again to find O'Brien looking at him with a very amused smile. Confused, he turned to look behind him to see a stunned zombie marine lying crumpled on the ground. "You could've told me!"

O'Brien broke into a full out laugh. "Where would the fun have been in that?"

Harvey the gate tech was in love.

* * *

><p><strong>13.45pm – North PierShield Emitter (9) Victor4-L **

John had just entered the room that housed the shield emitter as the siren sounded and door slammed closed behind him. He gave it an appraising glance over his shoulder before walking the few steps into the centre of the room and up to the Ancient device. He found the symbol to make the crystal tray open and then tried to recall the instructions he had been given. Usually his memory was near-photographic, but having a pretty serious concussion was putting a dampener on his mental capacity.

He identified the slot for the Ancient adapter cable and pulled the tablet PC he had been given from the slot on the back of his TAC vest. He plugged it and waited for the hardware to be recognised. He briefly remembered that he was also meant to rearrange a few crystals, but couldn't for the life of him remember which ones. He was close to giving up and calling for help when he noticed an icon flashing on the tablet screen. Curious, he clicked it, and was rewarded with a handy blueprint of the crystal tray along with instructions. "Thank you woman whose name I keep forgetting!"

He followed the instructions and activated the programme on the computer. It wasn't quite the plug'n'play he had been promised, but it had obviously been simplified down a lot so that he didn't have to do anything too complicated. He wasn't an idiot by any stretch of the imagination – he could have been MENSA after all – but having been blown up, beat up, stunned and the victim of his own stubbornness, he wasn't feeling like his usually smart self.

Eventually the programme ran its course and he unplugged the computer, slotting it back into his vest. He then clicked his walkie "This is Sheppard; I'm done with the first emitter, moving on to the next. How's everyone else doing?"

"_All of the first five emitters have been updated, and all the teams are en route to their next ones,"_ came a female reply. John really needed to remember her name. _"Dr. McKay and his team have just arrived at the maintenance room and I'm nearly done altering the life support system. This plan might _actually_ work."_

"_Of course it will work!"_ Rodney interrupted indignantly over the line. John waved his hand over the door control of the room, and as promised the previously secured door whooshed open. He stepped into the corridor beyond, stunner in hand, and began jogging as fast as he dared toward his next target. His ribs burned with the movement, but he was getting used to ignoring the pain by now. _"Are you saying you doubted me?"_

"_Uh…of course not…"_

"_I didn't hear you coming up with a better idea!" _Rodney replied. There then came a curse and a metallic squeal as he began working. _"Seriously, how many times have I saved this city now? Is anyone keeping count? No? Shall I tell you why? Because it's been _so many_ times! Surely by now you realise just how integral I am to keeping this…"_

"McKay!" Sheppard called forcefully, cutting the scientist off mid-tirade. "Get off the line unless you're going to say something important!"

"_Oh…right…"_ Rodney replied a little dejectedly.

"_Thank you, colonel,"_ the woman said gratefully, and a little smugly.

"_Hey! What's that supposed to mean…?"_

"McKay!" John called again. Seriously, it was like babysitting kindergartners.

* * *

><p><strong>13.10pm – Central TowerGenerator Room Bravo97-F **

Once 'Teyla' was returned to her claimed body she immediately climbed to her feet and scanned the room around her. She knew the two men would already be gone, but she was half-hoping that she had succeeded in shooting John Sheppard before he'd stunned her. She was disappointed to find herself alone – and _really_ pissed off.

How could it be so difficult to kill one man? How could he have thwarted her so many times? How could _she_ have _failed_?

In her anger she swung her fist into a nearby pillar, barely registering the pain such an immature move caused. She so desperately wanted to scream and kick and yell and generally throw a major temper tantrum, but she instead managed to restrain herself to simply nearly breaking her host's hand. She shook it distractedly as she tried to come up with her next course of action, her thoughts centering around all the different ways she could kill John Sheppard.

It was as she fantasising a rather brutal way of quartering him that an idea hit her. They had been relying on the city sensors to track down the Uninfected – but what about the smaller handheld life signs detectors? Sure, they required the gene to activate them, but there was a cell full of ATAs in the sigma tower that could easily be persuaded to help. All she needed was one of the devices.

A plan in mind, she headed purposely towards the primary weapons cache a few floors below. It had been emptied hours earlier when they had first been instructed to take arms, but as they were unable to use the Ancient devices they had been left behind. It would only have been a short transporter ride away; but as the power was out she had to take the stairs. Just another reason why she was going to enjoy killing Sheppard.

By the time she had arrived at the weapons cache, found herself a life signs detector, and travelled all the way to gamma tower and the nearest working transporter, nearly twenty minutes had passed. She hadn't once tapped into the Collective network, instead deciding to go solo – something she would never have even considered before. If she were honest, she didn't _care_ about the Collective anymore; sure, she wanted to prove herself still, and she feared the Voice more than anything, but she couldn't give rat's ass about its goals or whatever. All she cared about was John Sheppard – and the many ways she would kill him.

That very thought was what motivated her now. She prowled the corridors as if she owned them, ignoring the looks that a few of the other Collective members were throwing her as she passed. Word had already spread that she was a failure. Just wait until she presented Sheppard's decimated corpse at the Voice's feet – then they'd see.

As she arrived just outside the brig, she was surprised to see an entourage of people leaving; the Voice being the one in the lead. What was he doing down here? She stuck to the shadows as she watched them pause in the corridor ahead. The Voice was talking to someone she didn't recognise until she pulled the name from her host's database of memories. A grin twisted her features – his name was Barker, and he had the ATA gene.

She waited until the Voice had finished giving him his orders and turned to head off the opposite direction, leaving 'Barker' alone in corridor. He was obviously fresh meat; his posture was rigid and face completely blank – he probably hadn't even _begun_ assimilating. He marched in her direction.

Without making a sound she barrelled into him, dragging him into another room, slamming him against the wall and holding him there. He hadn't learned 'surprised' yet, but she suspected that's what he was experiencing. "'Barker', is it?"

He didn't answer, but she took his incredibly slow blink as a 'yes'.

"Excellent," she hissed. Still holding him like a vice with one hand she reached into her jacket to grab her stolen life signs detector. She pressed it into his hand. "Would you mind initialising this for me?"

The Ancient device gave a beep in reply and she held up both his hand and the screen so that she could see it. It was zoomed in, only showing their two dots and the handful that represented the Voice and his bodyguards. "Show me the whole city."

Again, 'Barker' blinked, and then learned the gesture for 'no' and shook his head. She slammed him against the wall again, but still he shook his head. "The device has a limited range," he answered in the perfect monotone of the newly awakened. 'Teyla' found it hard to believe that she had been this slow and basic only a few hours earlier. His lack of co-operation, though not his fault, frustrated her already short fuse. "I can expand the range slightly."

The device gave another beep and 'Teyla' studied the new screen. It now showed nearly a third of the city, the dots and floorplan outlines merging slightly as the device lost its accuracy; but she had found what she was after. Heading towards the North pier was a lone dot moving with purpose. Somehow she _knew_ that it was Sheppard. Who else would be stupid enough to move around alone in an infested city?

She bared her teeth in an animalistic smile. If 'Barker' had been more human, he would have felt fear.

But then her moment of ecstasy was ruined. A siren sounded abruptly, the door to their left suddenly slamming closed. A lockdown. 'Teyla' uttered a colourful Athosian curse word and released her death grip on 'Barker'. Though she knew it wouldn't work, she waved her hand over the door control to receive an uncooperative beep. She gave the door a good kick in anger and then paced away.

It was while her back was turned that 'Barker' had the wise idea to try and open the door himself. Still holding the life signs detector, he walked up to the door and waved his free hand over the door control. She heard the door open, and spun around.

She looked from 'Barker' to the open door and back again, stringing the two together. The grin returned to her face.

The hunt was on.

* * *

><p><strong>I love it when I accidently give myself a plot device – in my original plan Barker was never meant to join the Collective so Teyla just happened to find a way to find Sheppard – but this makes so much more sense! :P<strong>

**Oh, and for anyone that cares, Zelenka said (or at least, Google translate tells me he says) "Surrender you poor excuse for an astrophysicist" – not the best cuss in the world, but I think it suits him :D**

**See you next chap!**


	10. Assimilation and Altercation

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

I apologise profusely for the lateness of this update – it was a mixture of work, writers block and evil plot bunnies trying to steal my attention and make me write other things. You'll be pleased to know that I have come up with another fic (and several others) that I will plug at the end of this one, but I'm stopping myself from writing it until I have completed The Collective.

Again, I am doing my happy dance because I have SEVENTY-FOUR reviews which is just so awesome that I can do nothing _but_ dance with happiness. Thank you all for taking the time to read and review, you have no idea just how amazing you are!

I'm done gushing now – Enjoy!

* * *

><p><strong>Chapter Ten -:- Assimilation and Altercation <strong>

**13.50pm – Zeta Tower/Chair Room Yankee3-A **

Miranda McKinley was a record-breaker when it came to typing – she had once entered into a competition when she was briefly in college and had won by a landslide. She hadn't found the college that interesting (I mean...who has _typing_ competitions?) and had dropped out pretty quick; but it had proven that she was fast. So why now did she seem to be going so slow?

She couldn't figure out if her brain was going faster than her hands or if she was just imagining the difference – the fact that she was even wasting brain capacity thinking about it freaked her out a little. She forced herself to pause, breathe, and get going again. She tried telling herself that she was in her element; the lines of code running across the screen before her made more sense to her than anything. So what if she was under horrendous pressure to get this right and prevent practically the entirety of the city's population from being erased from existence and only leaving behind their empty shells in a vegetative state? She could totally do this.

"I can't do this."

"What?" Major Lorne, who had been hovering 'helpfully' behind her shoulder the whole time she had been working, answered with a hint of impatience. McKinley felt the tone like a knife in the eye but managed to ignore it; instead staring in horror at the tablet PC before her.

"There's not enough power," she replied, her voice almost breaking. She swallowed to try and clear her throat and explain when Lorne gave her an oblivious look. "The plan; it culminates with us activating the shield which will instead of creating a protective bubble will emit a strong energy pulse, right? Well, the shield has never been activated with anything other than a ZPM powering it, and was never designed to. Right now we're running on the back-up generators – one of which has been deactivated. We can't turn on the shield…"

Lorne nodded slowly, catching on to what she was saying. "So…what? We need to turn the generator for the central tower back on?"

"That still wouldn't be enough power, and even if it was, Colonel Sheppard still has the part needed to do that and he's on the other side of the city." McKinley explained as she resumed attacking the computer in the hope of finding another solution. "The alternative is re-installing the ZPM, but it will take time to do the switchover; time which we just don't have. I don't know what to do…"

Again, Lorne nodded and immediately reached for his walkie. McKinley expected him to be about to tell everyone the plan was a bust, but instead he called for McKay. She furrowed her eyebrows at him. Lorne smiled. "Don't ever tell him I said this; but Dr. McKay is our resident genius for pulling the rabbit out of the hat – he'll come up with something."

"_What is it? I'm busy here! Don't touch that Gull!" _McKay's irritated voice sounded out of the radio. _"Well, it starts with the same letter, doesn't it? Just back off and learn science or something!"_

Once Lorne had caught McKay's attention long enough he explained the situation in cliff notes and waited. McKinley made a few alterations to an algorithm she was finishing and then turned to listen to the empty static.

"_Alter the programs directive,"_ came the awaited reply. Lorne blinked in confusion, but McKinley could have kicked herself. _"Don't tell the system that you're activating the shield; mask it as a diagnostics that will activate every emitter to 'test' it but instead will emit the energy pulse. We only need it to be active for a few seconds, if that – it should work with the generators we've got. It means it will probably need to be activated manually using the chair though…"_

McKinley had tuned out the end of the explanation and was already working on re-writing thousands of lines of code that would create a simultaneous 'diagnostic' across every transmitter. It wouldn't be her usual eloquent work but it would do the job…hopefully.

"_Have you finished the air cycle program yet?"_ McKay asked once Lorne thanked him for the save.

"Yeah, it's all done," she replied, not taking her eyes from the screen while typing faster than she ever had in that stupid competition. "It should run a complete extraction and replacement of all the air on the city now that the lockdowns in place in under a minute. Everyone can hold their breath that long, right?"

Lorne nodded with a smile. "Except Torren, of course. But he's with Nakahara – she'll look after him with a hand pump if he needs it."

Things looked like they were finally back on track, and McKinley allowed herself to smile as well. As long as she could get this program to work they _could_ save practically the entirety of the city population from being erased from existence and only leaving behind their empty shells in a vegetative state…no pressure or anything. "How about you? How's the air filtration system coming?"

"_Faster than is humanly possible," _McKay answered. _"Considering I'm doing work that should in theory take days with only an out cold underling, a tablet PC with less RAM than a Dynabook and a useless brit that won't stop touching things! Seriously, Garner – touch that one more time…I don't care if it's not your name!"_

The transmission abruptly ended and the pair of them shared a brief grin. But then it was back to being serious and McKinley checked on the progress of the shield emitters. There were only four left to be updated. She turned to look at Lorne over her shoulder. "We'll be ready to go in about five minutes; you should get in the chair."

Lorne nodded and finally stopped being the constant presence at her shoulder, allowing her to focus on the program that would save the city.

_No pressure._

* * *

><p><strong>13.55pm – Sigma TowerHolding Cell Zulu2-C **

It had taken nearly ten minutes for Rowan Fletcher and Bruno Arrighetti to die. The Collective cell had attached itself to their brainstem, but had been unable to take proper control. Instead it had disrupted their entire nervous systems until the pain had grown so unbearable they had blacked out and fitted until death. It had been agonising to watch; and Carson couldn't even imagine how horrible it had been to experience.

He waited until their bodies had finally stopped spasming before he released the grip he had held on their shoulders in an attempt at comfort. He looked down at his hands to find them shaking uncontrollably and pulled them to his chest to still them. He was not ashamed of the tears that fell freely down his cheeks from witnessing the extinguishing of two lives.

After a while of just kneeling there between them, he eventually pushed himself up and onto his feet. He caught sight of Dr. Dharma who was sitting nearby, knees curled up to her chin, shaking as he was with a daunted expression on her paled face. He walked past her though, and made the few steps up to the bars of the cell – ten inches of steel between him and the guards. "They're dead."

The guards didn't react in the slightest, and Carson felt red hot anger replace the cold horror in his gut. "They're dead! I could've helped them but you wouldn't let me! Why wouldn't you let me? They're dead and you wouldn't let me help them! Why…I could've helped…I could've…"

"D-Dr…Beck-ket?"

Carson turned at Dharma's stammered voice, the anger fleeing him just as abruptly as it had flooded him. He knew it wasn't the fault of the soldiers outside their cell. For all he knew the real marines could have been erased by now and all that was standing there were shells controlled by the Collective. Fletcher and Arrighetti weren't the only ones to die that day. How many more souls would Atlantis lose?

He forced himself away from the cell door and let himself drop down next to Dharma. She leaned against his shoulder, trying to draw comfort from his presence, oblivious to the tears that were now staining his sleeve. He let her cry on his arm as he tried to order his own emotions that were threatening to overwhelm him.

He had so been hoping for a quiet day. When would this nightmare finally end?

* * *

><p><strong>13.55pm – Omega TowerMaintenance Room Juliet 67-R **

"Seriously Garner – touch that one more time..."

McKay snapped irritably at the excuse for a scientist currently messing with his well-constructed wiring job, unaware that his radio was still active. He was surrounded on all sides by a tangle of cables and machine parts as he improvised an update to the filtration system that would be able to trace the nanoscopic particles. Dr. Marcus Giles, supposedly an engineer with a degree from Oxford, gave him the same look he had earlier. "I don't care if it's not your name!"

Giles tutted in annoyance and then continued trying to correct him until McKay snapped and demoted him to helping Caruso with the new containment device. Eklund still lay stunned nearby, propped against a pile of equipment. McKay couldn't decide if the work would go faster or slower with him conscious based on his current 'helpers'. He heard Giles muttering about him but decided to ignore him and focus on saving the city…again.

Rodney hadn't been exaggerating when he had said that what he was doing should really have taken even him days to get done properly. He had had to practically dismantle the existing filtration system and put it back together again with a few adjustments, and then he had had to rewrite the program to identify the nanoparticles in particular. It would work…in theory at least. He looked back over at his underlings who were just finishing the containment device.

"Right, Gilroy…"

"You're doing that on purpose now, aren't you?" Giles interrupted as he and Caruso lifted the completed cylindrical device between them. McKay rolled his eyes and shoved a bunch of wires out of the way so that they could all access the filter.

"Just put the device here, and go away," Rodney instructed, and thankfully for his sanity, the pair of them did as they were told. Now it was just a case of attaching the cylinder and they were done. He risked a glance at his watch. He was both impressed with what he had achieved in under half an hour and painfully aware that even that could have been too long for some of the city's population.

As soon as he was done he leant back and activated his walkie.

* * *

><p><strong>14.00pm – Zeta TowerChair Room Yankee3-A **

"_The filtration system is ready to go,"_ McKay's voice came over the radio and Lorne let out a breath of relief. There was finally an end in sight to this day from hell. He confirmed the call and leant round in the chair to look at McKinley who was still typing fervently.

"We good to go, doc?" he asked, both eager to be done and a little anxious about being in the chair. He was used to interfacing with Ancient tech by now, but he never had been a fan of the chair. He could fly a jumper with ease, but there was a big difference between the space-barrels and an entire city – he always found himself easily overwhelmed by the volume of processes the chair controlled that all vied for his attention the moment he closed his eyes. He didn't understand how Sheppard could do it.

He saw McKinley shake her head and his stomach dropped. He _really _wanted this day to be over. She didn't look up from the computer when she replied. "We're still waiting on one of the shield emitters."

"Which one?" Lorne really wished he knew how to make the chair spin round so that he could actually face her without craning his head round the side.

"Number ten – its Colonel Sheppard's," she answered, finally putting the computer down and instead turning to another console. "I think I might be able to access the city sensors so we can track him…"

Lorne sat back in the chair and clicked his walkie. "Colonel, I hate to rush you, but we're kind of on a time limit here…"

"_Yep, I'm aware of that, Major,"_ came Sheppard's short reply.

"Wait…can everyone tell me where they are please?" McKinley suddenly tapped her own walkie so that she addressed all of the ATAs. Lorne gave her a curious look as a chorus of locations sounded over the radio. She gestured at one of the Ancient screens that had a map of the city on it along with hundreds of blips representing human life signs. "There are too many dots moving around the city."

Lorne furrowed his eyebrows and pushed himself out of the chair to come and stand next to her. He couldn't do anything until the last emitter was programmed anyway. He studied the screen, matching most of the dots to the locations, but he quickly caught on to what McKinley was seeing. There were two dots in the North East section moving through the lockdown that weren't part of their resistance group. "Crap…Sir, there are two unidentified contacts nearing your position."

"_Definitely not ours?"_

"Definitely not," McKinley answered before Lorne got the chance. "But they're moving through the lockdown which is completely impossible unless they've got the ATA gene."

"Or one of them does; we left at least five of us in enemy hands," Lorne added, the guilt he had just about pushed aside coming back again. He was going to need some serious therapy if they ever got out of this.

"But why are they the only ones moving? Surely they would be sending more than two people to try and stop us, and why are they only heading after the colonel? It doesn't make sense."

"_It's Teyla."_

* * *

><p><strong>14.00pm – North East DockSection Victor Level 4 **

It was just typical that the first trait 'Barker' learned from his host was cowardice. "Shouldn't we have told The Voice that we had a way to move through the city?"

'Teyla' clenched her fists and counted down slowly from ten, reminding herself that it was easier for him to be conscious and walking by himself than for her to be dragging his dead weight around. She purposely doubled her pace making the scientist practically have to run to keep up with her. She didn't answer his question, hoping that her annoyed silence would be enough for him to realise he should keep his mouth shut.

It didn't work. "We should be connected to the Collective, going silent like this will anger the Voice."

Man, he had learned to talk fast. She kind of missed the silent robot he had been less than ten minutes earlier. At least then he had just done as he was told instead of questioning everything. "And just what is the Voice going to do? It and everyone else in the Collective is currently trapped and helpless. All you have to worry about is what will happen to you if you continue to make _me_ angry."

There was a silence as 'Barker' considered her words. Apparently his fear of her outweighed the potential wrath of the Voice and he fell into obedience. After a while of just following her like a puppy dog, he checked the life signs detector again. "He's on this level, only a few corridors over."

'Teyla' felt her features stretch in the vindictive smile she always got when she thought of how she was going to kill John Sheppard. Not long now, he was so close she could almost feel him. Oh, how he would pay for what he had put her through that day. She had only existed for mere hours and yet she was filled the hate of a lifetime.

"He's on the other side of this door."

"Excellent. That'll do 'Barker'." 'Teyla' brutally and suddenly struck him across the back of the head and the scientist crumpled to the ground. She had been itching to do that. She then grabbed his arm and passed his hand over the door control.

_Finally._

* * *

><p><strong>14.00pm – North East DockShield Emitter (10) Whiskey4-L **

"_It doesn't make sense."_

Well, actually, it made perfect sense. There was only one person, that John was aware of at least, that seemed intent on hunting him down that day. He should have known that Teyla, or whatever it was that was currently possessing her, would be resourceful enough to find a way through the lockdown.

"It's Teyla," he replied without a trace of doubt. Maybe the others picked up on his tone even over the bad quality of the walkies because they didn't question his assessment. As he entered the room that housed the last emitter he wasn't in the slightest bit reassured by the closing door behind him. He briefly considered disabling the lock, but he was well aware that everyone was waiting on him now and he figured he didn't really have the time.

He crossed the distance to the emitter and quickly ejected the crystal tray. He was a lot quicker the second time round and didn't have to address the blue prints. He had the tablet computer plugged in and uploading the programme in under two minutes. It was as he was staring intently at the progress bar, willing it to move faster, that he caught a flicker of movement in the screen's reflection.

He hadn't heard the door…why hadn't he heard the door?

It was just enough warning for him to duck the first blow that would have smacked his head into the shield emitter. He pushed away from the device and behind his attacker and then immediately drew the Wraith stunner from his holster. Before he could get a shot off however a flying foot knocked it from his grasp. Teyla was a lot faster than she had been that morning. He was so screwed.

Adrenaline is an amazing thing, he concluded, as he managed to put a day's worth of serious injuries to the back of his mind and focus on not getting any more – or at least trying not to. He blocked a handful of blows that would have sent him to the land of milk and honey if they had connected, but wasn't gaining any ground himself. It was almost as if they were evenly matched; but John knew that even on a good day he couldn't beat her…was she toying with him?

He struck out with a fist that through some miracle actually found its mark. Her head whipped round from the impact, a thin trail of blood escaping her lips. He actually felt a little guilty, but he should've known that she could hit back twice as hard. He received an elbow to his right cheek that sent pain blooming in his already pulverised head and stole the colour from his vision. He staggered back, just about remaining on his feet, presenting himself as the perfect target – but for some strange reason, she waited.

He blinked through the pain that was making the world sway around him to see her simply standing there in a ready stance, just waiting. For someone who desperately wanted to kill him half an hour ago she was sure taking her time. He guessed from her cruel smile that it wasn't a change of heart that was making her go easy on him – she was just drawing it out.

As he was trying to force his addled brain to come up with a solution he heard the tablet PC give a contented beep. A millisecond later his walkie squawked _"Sheppard, the programme's uploaded; you've just got to initialise it!"_

Teyla cocked her head at him curiously, and then followed his gaze to look at the emitter behind her. It was just typical that all he had to do was press the damn Enter key and maybe, _just maybe_ he might be able to finish this day somewhere other than the morgue. It was sod's law that Teyla would happen to be standing between him and said Enter key, and by the grin on her face he could tell that she knew.

This was_ so_ not his day.

His equilibrium almost regained he closed the gap between them, a combo in mind that would hopefully take her out long enough for him to hit the damn key. It didn't work; she blocked the first punch, grabbing his right fist and twisting his arm behind him. His ribs screamed from the abuse and he thought for a horrifying second he was going to black out. Instead, he managed to smother a real scream into a strangled cry as his shoulder was wrenched from its socket.

There just didn't seem to be a curse word in two galaxies that truly reflected the pain he was in so he just swallowed the tirade of swearing as she shoved him to the ground. Adrenaline wasn't working so much as a pain killer now – in fact, it was pretty much useless. His vision still hadn't stopped swimming from the hit to the face, his ribs hurt to the point that he was fearful to breathe and his shoulder hurt so bad he couldn't even compare it to anything.

And he still needed to hit that god damn button.

She was waiting for him again as he lay on the ground trying to convince himself that breathing was necessary despite the pain it caused. After a few seconds he managed to push himself onto his working hand and knees, halfway towards his goal of standing up. He could feel her eyes studying him as he worked up the strength needed to pull off what should have been a simple manoeuvre. It seemed to take forever, but he just about made it to his feet again.

He staggered, his balance greatly impaired, as he scanned the area. His stunner had flown to the other side of the room and he doubted she'd let him reach it even though she was toying with him. He still had the 9mm that she had held to his head a few hours ago, but he didn't have the resolve to use it and he knew that Teyla would know that as well, making threatening her a pointless exercise. Besides, he'd have to draw it with his left hand from his right leg – an awkward move even for someone without a whole bunch of broken ribs.

His mind gave him only one option. He didn't like it, but without a concussion stealing away sensible thought processes he doubted he'd be able to come up with anything better.

He tackled her. Literally. With a burst of speed he didn't even know he could pull off in his state he ran the short distance between them. Ignoring every injury that was screaming at him for his own stupidity he hunkered down and rammed his good shoulder into her gut, doubling her over with a surprised grunt.

They landed in a heap on the floor less than a foot from the shield emitter. Her head had hit the concrete on impact, dazing her long enough for him to drag himself close enough to the computer and reach for the key.

_Finally._

* * *

><p><strong>14.05pm – Zeta TowerChair Room Yankee3-A **

"Activate the shield!"

McKinley yelled over her shoulder once the final shield emitter came back online. She had been watching the two dots on the sensor screen dance around each other, silently praying that Sheppard really was the guy she had heard all the stories about. She guessed they were true when he succeeded in his task despite being assaulted by the legendary Athosian fighter.

Behind her Lorne was reclining in the Ancient chair focusing his energy on the process of turning on the shield. She studied her computer screen, crossing her fingers that her faux-diagnostic programme would be enough to trick the shield emitters into activating.

She was rewarded seconds later when a blue sheen of energy washed across every square foot of the city.

* * *

><p><strong>14.05pm – North East DockShield Emitter (10) Whiskey4-L **

Teyla recovered from the inelegant tackle quickly, a mask of fury on her face. John realised that she was no longer going to toy with him – she was just going to kill him. Maybe the thing possessing her could tell that it was nearly the end but refused to go until she had finished what she'd started.

He attempted to get up and away from her, but the adrenaline had left him and all that he was left with was exhaustion. He dragged himself painfully less than half a metre away before she flung a kick into his ribs that rolled him onto his back. He was hissing through clenched teeth from the hit, his attention stolen by the focus required to breathe rather than trying to fight back.

When he opened his eyes slightly he found her looming over him, straddling his chest. She then wrapped her hands around his throat, cutting off his air supply.

He stretched up with his good arm to try and push her off, but he was so weak she'd paid his hand no heed. His right arm, which he could barely move, reached for his thigh holster, but as he wrapped is hand around the butt he knew he'd never be able to pull the trigger. He let his hands drop, the fight leaving him along with his strength.

John stared up into Teyla's eyes trying to find the real her behind the mask of hatred currently choking him. He wanted to tell her that it wasn't her fault. He wanted to tell her that she shouldn't blame herself for killing him. He wanted to tell her that he loved her.

Any words were stolen from him before he could even form them as his throat was constricted. His vision began to tunnel, the grey edges closing in around her face.

He let his eyes close, and the darkness claimed him.

* * *

><p><strong>Yes, I am actually that evil that I am going to leave it right there. <strong>


	11. Guilty and GuiltRidden

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

Hopefully this was a fast enough update! I loved the fact that out of the ten reviews I received for the last chapter, the majority of them were declaring me pure evil or or people telling me they hated me! I felt the love :P

Now this is the beginning of my two-part epilogue that should hopefully tie up the millions of lose ends (such as Sheppard being a little...well...) and should prevent me from rushing the end in my desperation to start writing the next fic I've got in mind.

But you're probably not even reading this as you are desperate to find out what happens to Sheppard, so nevermind! And Enjoy!

* * *

><p><strong>Chapter Eleven -:- Guilty and Guilt-Ridden <strong>

**14.07pm – North East Dock/Shield Emitter (10) Whiskey4-L **

From her distant perspective from the very back of her own mind Teyla had seen the final moments of her possession. She had witnessed the acts of cruelty inflicted by her hands, yet had had no power over her actions. She couldn't even struggle, not with all the will in the world. She had simply been made to watch, her shouts of protest sounding quiet to her own ears. She had cried and screamed, hammering on the walls of her prison as she had choked the life out of John Sheppard.

And then it had all been taken away with a flash of blue, sending her spiralling into darkness.

When she awoke again she found herself slumped on top of him, her hands still wrapped loosely around his throat. She felt no movement beneath her grip. He wasn't breathing, and if he had a pulse she could not feel it. She immediately threw herself off of him to kneel at his side, panic enveloping her.

How long had it been?

"John!"

She flew on instinct, praying that it hadn't been that long. She unzipped his TAC vest and began the compressions on his chest, although she almost stopped when she felt a rib buckle beneath the force. She counted under her breath to keep herself in rhythm, only pausing to lean down and breathe air into his mouth. Every second that passed with him lying lifeless beneath her hands felt like hours. She didn't know how long she kept going, dread and guilt building inside of her, but stubbornness and desperation prevented her from stopping.

And then suddenly he shot up, gasping for the air he had been deprived of for so long. She wrapped her arms around him in relief, providing him with an anchor as his disorientated eyes darted around them. They stayed like that for a moment, caught in the embrace while John gratefully breathed deeply against her shoulder. "Thank the Ancestors," she whispered into his neck.

After a few seconds, the adrenaline from his brush with death must have run thin because he groaned with pain and sagged against her. As carefully as she could she laid him back down, studying his tired face as he scrunched his eyes shut with pain. When he opened them again, he barely whispered her name through his damaged throat "T-Tey-la?"

And then the guilt hit her with more force than she had ever thought possible. There was a hint of something in his eyes as he looked up at her – it wasn't quite distrust, but it was near enough to wrench her heart. She took a hold of his hand and held it in her lap, trying her best to smile reassuringly. "It's me," she promised, wishing for the uncertainty in his gaze to leave.

He gave her a smile that was as close to his usual charm as he could manage in return, and the smallest of weights was lifted from her chest. Maybe it was that which led to her next action. Maybe it had been a day of helplessness and inaction as she experienced life through another's eyes. Maybe it was just that she was caught up in the moment; or maybe, just maybe, she had finally come to the forgone conclusion that was their first meeting almost five years prior.

Without warning, she leaned down and kissed him.

At first John tensed, the sudden act taking him by surprise, but then he relaxed and kissed her back. In that moment Teyla felt as if she could forget everything and she knew that as long as she had John Sheppard she would be okay. She wouldn't allow her practical mind to interfere with thoughts of Kanaan, even though a pang of guilt over Torren almost made her pull away. Eventually the kiss ended when it became apparent that John needed to breathe, and she pulled back with a legitimate smile.

It was only then that she allowed a logical thought to impede her emotional impulse. _Things just got complicated._

And then the walkie attached to his open vest squawked, stealing the moment away. _"Colonel Sheppard? Do you read? Colonel?"_

John gave her a final look, his gaze entirely free of the distrust, before he let his eyes drift closed again, giving in to his exhaustion. She gave his hand a squeeze and then took the walkie to silence the slightly panicked demands for his attention.

"This is Teyla; I am going to need a medical team to the North East dock."

* * *

><p><strong>14.15pm – Sigma TowerLevel Four – Section Zulu**

When Richard Woolsey finally came to he had no idea where he was or what had happened. He blinked at the unfamiliar surroundings - 'confused' nowhere near adequately describing how disorientated he felt. He remembered being in the control room as the explosion was called in, and then…nothing. He checked his watch, concerned to find that nearly four hours of his life had disappeared. He pushed himself onto his elbows, finally seeing that he wasn't alone. "What happened?"

Ronon was already standing; all senses on alert as he scanned the corridor. Two bulkheads had closed on either side, effectively trapping them. He shrugged tersely at Woolsey, obviously not comfortable with waking up in a strange place and being confined with no explanation. It was a little unnerving, to put it mildly. Dr. Keller woke up nearby, and once she seemed alert enough, Ronon offered her a hand to help her to her feet. There were also four marines and a scientist with them, all in varying stages of 'what the hell?'

Woolsey figured that it was his job, as leader of the expedition, to get them some answers. He got to his feet unaided, not that Ronon had offered, and reached for his earpiece. "This is Woolsey, would someone mind filling me in please?"

There was a pause over the line. _"Sir, this is Amelia in the control tower, and we're not sure what happened…no one appears to have any memory of the past four hours, the central tower has no power and the city appears to be in lockdown."_

Well that wasn't good. "Understood," he replied, but only as an acknowledgment and not because he had _any_ understanding of their situation. He felt the eyes of those he had been trapped with stare expectantly at him as if he were meant to pull off some miracle. Instead, he decided to test the lockdown theory and stalked over to the door control.

"I already tried that," Ronon grunted irritably. Someone had woken up on the wrong side of the amnesia-inducing blackout. Woolsey ignored him and waved a hand over the control regardless. He was rewarded with a stubborn bleep telling him that the door did indeed refuse to open. "Told you so."

Again, Woolsey ignored him and instead reactivated his earpiece. "Is there any way to override the lockdown or manually open the doors?"

"_Negative Sir, the whole point of the lockdown is to keep people from moving around the city freely," _Amelia answered, stating the damn obvious in answer to his truthfully stupid question. He was much better at making corporate decisions rather than figuring out how to deal in the aftermath of an explosion and unexplained time-lapses.

"_Mr Woolsey, come in, this is Major Lorne – can you hear me?"_

"Loud and clear, major. Care to tell me what's going on?" Woolsey answered, thankful for the distraction from his own shortcomings as a military strategist.

"_Not sure you'd believe me, Sir, but I'll do my best to explain," _Lorne replied, exhaustion and relief evident in his voice even over the radio connection. Woolsey, along with everyone else in the corridor, instantly had their attention grabbed by the promise of an explanation. _"During the explosion a nano culture was released that then possessed around 90% of the city's population."_

Woolsey blinked. "Excuse me?"

There was a hint of smile in the major's voice when he answered. _"I know it's pretty hard to believe Sir, I'm having trouble with it myself and I've been conscious the last four hours. We're deactivating the lockdown now, there's going to be one helluva clean-up after this."_

True to his word, a short siren sounded and the two doors blocking them in receded into the walls. Woolsey eyed the freedom warily, not 100% sure that he really wanted to face the 'clean-up'. But, he was the leader of the expedition, and as such he would deal with whatever awaited him. He threw Ronon and Dr. Keller a look that hopefully didn't show his trepidation, and then he boldly stepped into the aftermath of a day he was almost glad he didn't remember.

* * *

><p><strong>14.05pm – Sigma TowerHolding Cell Zulu2-C **

Carson was lost in his own thoughts, his face betraying none of the emotions warring below the surface as he stared at the cell wall opposite. He was careful not to let his eyes stray to the two corpses that he and Dr. Dharma shared the space with – he didn't think he could handle it.

It wasn't the first time he had watched someone die, and though he strongly hoped otherwise, he doubted it would be the last. As he sat there, frozen in an attempt to keep himself from breaking, his mind trudged up the faces of every person who's last moments he had witnessed. His heart ached when he thought of Perna and the rest of the Hoffan population, killed by their own desire to stop the Wraith. He thought of every patient he had ever lost on the table. And then he had to squeeze his eyes shut when he thought of the girl Michael had killed to get his co-operation.

When would it stop?

With his eyes still closed he felt, rather than saw, the wave of energy that pulsed throughout the city. He opened them again, glad for the distraction, just in time to see the handful of marines stationed outside the cell to collapse. His instinct was to get up and help them, but logic reminded him that there was a cell door between them and so he remained seated, Dharma still pressed against his shoulder.

And then the air was stolen from them. There was a whine like a turbine starting up and a breeze picked up around them, sucking the air from the room. Carson had the sense to take as deeper breath as he could before it was all gone, wrapping his arms around Dharma as she began to panic beside him.

His chest burned and his throat dried as the pressure of holding onto the last lungful of oxygen built up. He didn't know how long they were left deprived for, but it felt like hours. The strength began to leave him as his vision greyed and tunnelled, threatening to knock him out. He felt Dharma sag against him as she succumbed. As he sat there, fighting to stay conscious, he briefly wondered why he was bothering. It was a dark thought that he hoped he wouldn't have when he was no longer oxygen-deprived, but it crept up on him regardless. He almost let out the breath he'd been holding, letting his eyes slide closed.

And then literally, a breath of fresh air filled the room. The whining of the turbine cranked to a mechanical halt and then resumed in reverse, pumping the clean air back in. Despite his previous thoughts, Carson found himself hungrily gasping in the air, filling his lungs gratefully. A headache remained and his chest still hurt, but he felt human again, and he turned his attention to Dharma. She'd begun breathing on her own, though remained unconscious against him. He decided that she deserved a moment of respite and allowed her to sleep.

He glanced over at the marines who were still crumpled on the ground, relieved to see that they were breathing as well. Carson really hoped that the whole episode was the plan to save the city – he didn't think he could handle much more.

Around ten minutes passed with him just sitting there, waiting. His thoughts got dangerous again as he accidently let his gaze stray to the dead, but he managed to pull himself out of the downward spiral before it got too bad. Eventually, the marines by the door began to wake – well, at least most of them did.

Carson didn't know their names, they were new recruits that he had yet to be acquainted with, but he watched as they looked at each other in confusion. A young brunette crouched beside an older soldier, nudging him. He didn't react, and Carson instantly knew that the real soul that was meant to inhabit that body was long gone. Another life lost. Still confused, the brunette pushed herself upright, finally seeming to realise where she was. She turned round to look in the cell, seeing Carson and the others for the first time. "You mind telling me what's going on?"

Carson almost smiled. If it wasn't for the fact that he had yet to learn the full consequences of that terrible day, he might've managed one of his friendly smiles, but as it stood he settled for a relieved smirk.

It was over.

* * *

><p><strong>16.00pm – Central TowerWoolsey's Office **

"How many?"

Lorne already stood at attention before Woolsey's desk, but at the bluntness of the question he straightened even more. He had reverted to professional soldier as he had dealt with the aftermath, afraid that if he were true to himself he wouldn't be strong enough to hold it together. He had co-ordinated the clean-up, directing the injured to the main infirmary and the dead to the auxiliary. He had had the job of counting the bodies.

"Fourteen confirmed dead. Fifteen left in a vegetative state. Twenty-seven injured."

Woolsey closed his eyes, almost as if he had flinched at the numbers. Lorne had brought him up to speed with a clipped report that made it obvious that the events were taking their toll on the major, despite his best efforts to hide it. He knew about the explosion, the infection of the _Alcoloniavarium_ culture and the consequential confusion that being attacked by their own had caused. He was aware of the friendly fire incidents – Lorne hadn't been the only one faced with the difficult choice. Dr. Beckett had also informed him of the experiment performed in the holding cell, and judging by the lack of eye contact the doctor gave him, Woolsey had assumed his involvement as well.

He suspected their most recent psychiatrist was going to be in high demand in the near future. Woolsey was thankful that he couldn't remember his actions.

"Those in the vegetative state, does Dr. Beckett think he can help them?"

"He doesn't hold out much hope," Lorne replied, staring stubbornly at the wall above Woolsey's head. "McKinley and McKay have been studying the database entry and say that the Ancients couldn't figure out a cure either. Beckett is keeping them on life support for the time being."

"I will be making my report to the SGC as soon as Dr. McKay reinstalls the ZPM," Woolsey rubbed his chin uncertainly. It was obvious that he was not looking forward to it. "I suspect that they will request we send them back to Earth, along with the…along with…"

He couldn't bring himself to finish the sentence. Lorne gave the smallest of nods to show that he understood, and then resumed his cold stare.

"There will be a memorial service the day after tomorrow," Woolsey continued, his tone sombre. "That should allow the injured time to heal so that they can attend. Has there been any news on Colonel Sheppard?"

"He's in surgery at the moment," Lorne's voice was almost monotone, the emotionless timbre not suiting him. "Dr. Keller and her entire staff are working hard to see to all the injured. The infirmary is not honestly equipped to handle so many."

"Let's just hope they never have to again."

* * *

><p><strong>17.00pm – New Athos <strong>

Teyla stepped through the gate with Torren perched on her hip, a nervous expression on her face. Maybe Torren had picked up on her odd mood, because he didn't seem as excited as usual by his trip through the wormhole. Instead he buried himself against her shoulder, unnaturally quiet.

Earlier, once John had been safely shipped off to the infirmary and Keller's care, Teyla had practically pounced on Lorne to question him about Torren. She had known that he was safe as long as John was looking after him, but not knowing where he was scared her. Lorne had directed her to Dr. Nakahara in the Zeta tower who, after a brief conversation about Torren's good behaviour, had immediately ran off to help with the influx of injured following the explosion and subsequent madness.

Torren had been pleased to see her, but he had been subdued as if he could pick up on the inner turmoil in his mother's mind, and considering the Wraith DNA she had passed to him, that wasn't such a stretch. Even now as she took the reluctant steps required to reach the settlement she could not get her thoughts to settle. So much had had happened in such little time; she wished she had had a reprieve in which to focus before she had had to face Kanaan. She did not know what she would say. Though emotionally her decision was made, her logical mind kept throwing up hypothetical road blocks, making her second guess herself.

All too soon, she reached the outskirts of the settlement, a gathering of her people already there to welcome her. They had been concerned, and rightly so, and her presence there with Torren eased their worries. She was surrounded by words of kindness as her people gave thanks to the Ancestors for keeping her and Torren safe, but she could not bring herself to acknowledge them beyond the polite smile on her face. It was not the Ancestors who had saved her and protected her child.

She made her way through the crowd that then began to disperse, leaving her alone with Kanaan who had held back. He had a strange expression on his face, but it disappeared as he relieved Torren from her grasp. He hugged the boy close, his relief palpable. "Thank the Ancestors that you are safe."

"Kanaan…" Teyla began, but she had no idea how to finish. She watched him with their child and felt the weight of guilt bear heavily on her shoulders. He looked up at her, and there was the odd expression again. "I am sorry for the scare this must have put you through. It was never my intention."

It wasn't she had been going to say, and they both knew it. Kanaan stroked the back of Torren's head. "Life is unpredictable." Was all he said. They stood like that for what seemed like eternity, trying to think of something to say to fill the distance that had been growing between them for some time.

"I…I have…"

"I have known for some time, Teyla," Kanaan interrupted before she could even finish stammering. She looked at him in surprise, half-hoping and half-dreading that he was talking of the same thing she was thinking. "Even before we…before we joined together…I always knew your heart truly belonged to another. It is only now that you seem to realise this truth as well."

"I am so sorry…" was all Teyla could think to say. Part of her rejoiced that she hadn't been the one to say it, while the rest of her cursed her weakness. Kanaan gave Torren another hug, and then handed him back over.

"I am sorry too," he whispered, regret evident in his eyes. "For I have always loved you. I love you enough to be honest with you. I love you enough that I will let you go, so long as you are happy."

Teyla gave a small smile. "You have never made me sad."

Kanaan nodded slightly, and took a step back. "But that is not enough."

Teyla watched him walk away, praying that her heart had made the right choice.

* * *

><p><strong>20.00pm – Central TowerInfirmary **

John Sheppard was way too used to waking up in the infirmary. Even before he opened his eyes he recognised the sounds of the machines, the hushed whispers of the staff and the odd sensation of painkillers pumping through his system. He managed to open his eyes without being blinded as the lights had been lowered, a sign he took to mean that it was later in the day. He was grateful for that small mercy when even the low light sent daggers of pain into his skull.

"Lorne told me what happened."

John blinked, recognising the voice but not able to match it with his hazy vision. He took a moment to allow his drug-addled brain to catch up, and then turned to look at the massive blur sat beside his gurney. Ronon was sitting straight backed on a plastic chair, staring intently at the floor. Even through the haze, John could see the guilt on his face. He struggled to remember what had happened; but all his mind felt like telling him was that he'd lost his memory a couple of times that day. Not helpful. He kind of wished that Lorne had felt the need to fill him in too.

"Beckett told me some stuff as well. I…I did some really bad…that doesn't even begin to cover it. I…"

Ronon trailed off, leaving John none the wiser as to what they were talking about. He opened his mouth to tell him so, but his throat was so dry and swollen he couldn't even manage a grunt. Obviously the tiny sound he had made was enough to grab Ronon's attention. The big Satedan hadn't realised that John was awake, and now he knew he shifted awkwardly. John berated himself for moving; he had unintentionally interrupted Ronon's confession, and he doubted he'd hear the rest of it.

Ronon glanced away, trying to come up with something to say. Usually John would have said something flippant by now and they could've moved on, but talking wasn't going to happen any time soon. The painkillers were keeping him from feeling the full extent of injuries, but he knew from the slightest movements he could achieve that they were numerous and serious.

And then Ronon surprised him. "I'm sorry."

John really wished he could talk. Not that he would've known what to say, but he at least wanted to tell the guy that he had no idea what he was apologizing for. He'd probably ask something along the lines of 'what the hell happened?' but wasn't sure if that was really appropriate considering Ronon's guilt-ridden expression.

"Teyla can remember what happened; she says she was awake the whole time but was powerless. I can't imagine…its bad enough just knowing without…" Ronon trailed off again, his eyes falling back to the floor, his shoulders sagging. It was just so uncharacteristic to see the Satedan look so beaten and for a moment John didn't want to know what had happened. "How did you deal, after Thalen, I mean? Does telling yourself that it wasn't you actually work?"

Fragments of memory began sliding into place. John remembered being in a hallway, Teyla holding a gun to his head…but it wasn't her. Everyone was different, possessed, but they had a plan…and…did it work? It must've worked, right? Cause Ronon was normal again and not…trying to beat him to death…oh. That explained the apology.

John gave his head a slight shake, ignoring the pain the movement caused. It was the closest he could get to communicating, and he needed to answer the question. He wanted to tell Ronon that it was alright, but he wouldn't give empty reassurances. Even now, nearly three years on, he still felt guilty over the Thalen and Phoebus incident.

"Thanks, for not lying," Ronon muttered. He then pushed himself up and out of the chair. "Teyla said she'd bring Torren by later when she got back from New Athos, and McKay said something long-winded about being in high demand and that he'd see your stubborn ass later. I…I gotta go."

John gave a half-smile, and then watched as Ronon practically fled from the curtained off section, leaving him alone. He got the feeling they'd be picking up the pieces after this one for a long time yet.

* * *

><p><strong>20.30pm – Central TowerZPM Room Zulu1-A **

"Well that's strange."

Zelenka looked up from his own computer to glance curiously at McKay. The pair of them had been practically trapped in the ZPM room since power had been restored to the central tower and Woolsey had ordered them to re-install the ZPM. McKay had been reluctant to do so, his own words ringing in his mind:

_It was lucky I pulled the ZedPM and switched to back-up generators or the explosion could potentially have taken out the whole tower…_

They still weren't sure what had caused the power fluctuations that had in turn caused the explosion, and Rodney wasn't willing to switch back to the ZPM until he was certain history wasn't going to repeat itself. And judging by what he had just found, it was a good thing he hadn't.

"What is strange?" Zelenka took the bait and asked when Rodney didn't immediately fill him in. Rodney kept the suspense going a little longer, completely unintentionally, as he double checked what he was seeing. "Rodney?"

"Hmm? Oh," Rodney glanced up from his computer, a frown deepening his brow. "Those power fluctuations you were complaining about…I just found out what caused them. There's a subroutine in the power directory that's creating random build-ups in parts of the central tower's system. That's what caused the explosion earlier. It's designed to target areas with the highest potential for the biggest boom, but something must have gone wrong with it because the actual explosion wasn't that big…"

"Wait, 'designed'?" Zelenka interrupted. "So you are saying…"

"Yes Radek, I'm saying that this was done on purpose," Rodney huffed, and then looked back at his screen. "And I recognise the code…"

* * *

><p><strong>Let me know what you think! Reviews are like my food supply, I shrivel without them :P<strong>


	12. Consequences and Condolences

**Stargate Atlantis -:- The Collective**

**Author's Note(s):**

Okay, this is the last chapter of this epic that has been my longest and most highly reviewed fic ever! Thank you so much to everyone who has read/reviewed/favourited and/or alerted this fic – without you I would have given up 50,000 words ago :P Revel in your awesomeness, you deserve it!

And briefly, to sheppardlover928: I have two bullshit answers to your Woolsey question – One: he just wanted a general answer as to what the hell had happened so he just asked everyone with a radio, and Two: technically, Lorne was/is acting military commander, so _really_ Woolsey should've called him (Honest answer – I don't have a clue, didn't actually think about it :P – hope that helps lol)

Super thanks again! Enjoy the last chap!

* * *

><p><strong>Chapter Twelve -:- Consequences and Condolences<strong>

**22.00pm – Gamma Tower/Quarter Charlie79-H [Lorne's Quarters] **

_Dear Mrs Walters,_

_I am writing to inform you with the deepest regret that your husband, Sargent Henry Walters, has been killed in the line of duty. I am afraid that the circumstances that led to this tragic loss are classified, but I hope you can find solace in the fact that it was an act of true heroism for which he was sacrificed, and that you can be forever proud of your husband._

_As his superior officer and friend, I can say with great sadness that Henry will be sorely missed, and we will suffer from his absence. Sargent Walters was deeply respected and liked by all who had the privilege of knowing and working with him, his sense of humour in the face of uncertainty and his unabashed bravery were legendary._

_I offer you my most sincere condolences for you loss. God bless his soul in eternal rest. _

_Yours Faithfully,_

_Maj. Evan Lorne_

_United States Air Force_

It couldn't have been further from the truth – the first paragraph at least. Lorne was sorely tempted to throw the offending laptop and the fake letter across the room, but he knew it wouldn't achieve a thing. They wouldn't let him rewrite the Dear John with the truth just because he threw a temper tantrum and smashed up an expensive computer; even if the act might have made him feel a little better.

Instead he saved the file and emailed it to Amelia in the Control Tower who would then attach it to the next data burst back to Earth. The letter was a precaution only – Lorne fully intended on being the one to inform Mrs Walters face-to-face, but that was dependent on whether Woolsey would grant him leave. With Sheppard out of commission he was the Acting Military Commander of Atlantis, which probably put a dampener on his chances.

He would consider going AWOL if he had to.

But then again, if it felt so wrong to lie in a letter, how much better would he be at lying to her face? He couldn't tell her the truth, the non-disclosure agreement that everyone on the expedition had signed made sure of that, but he couldn't just tell her nothing. How could he give her closure when all he was giving her was empty words? How could he tell her what a great man Sargent Walters had been when he _knew _that he was the one who had killed him?

Even now he kept replaying the moment over and over, his mind cruelly offering him alternative scenarios where he could have avoided the bloodshed. If only he had done things differently… If only Walters hadn't shifted those few inches to the right… If only he had never woken up that morning.

He pushed the laptop to one side and lay back on his bed, staring up at the intricate ceiling. The day was finally over; but he got the feeling he'd be feeling the consequences of this one for a long time yet.

* * *

><p><strong>[The Next Day]<strong>

**08.00am – Central Tower/Conference Room **

"Dr. Beckett is working as hard as he can to try and help those that are…those that are on life support," Jennifer concluded as she came to the end of her report. Rodney squeezed her hand under the table in reassurance as her voice caught, and she passed him a grateful look. "But to be honest, it doesn't appear as if there is anything that we can do."

Woolsey nodded, and decided not to push the matter further. "I will inform the SGC of the situation; once Dr. McKay sees it fit to reinstall the ZPM of course…"

Rodney's stomach dropped as Woolsey turned his focus on him; a hint of annoyance in his gaze from what he perceived was Rodney stalling. The truth of the matter was that he had spent the whole night combing the city's systems for more of the code that had caused the explosion, as well as quadruple checking that he was right about the culprit. He had yet to tell Woolsey anything other than that it wasn't safe to install the ZedPM – it was dangerous enough with just the generators – or that he knew who had attempted to destroy Atlantis.

Across the table, Zelenka gave him a look. They were the only two who knew.

"I haven't reinstalled the ZedPM because it isn't safe, unless you'd like a repeat of yesterday's horror movie?" Rodney defended with sarcasm that wasn't wholly necessary. He felt the atmosphere in the room shift and knew he'd said the wrong thing – but he wasn't exactly one to take back his words. It was Jennifer who squeezed his hand then, a warning for him to tone it down.

"I don't think anyone wants that," Woolsey replied quietly. Next to Zelenka sat Lorne, who seemed to have gotten a shade paler following Rodney's comment. "Now if you'd care to explain _why_ the ZPM is unsafe, please?"

Rodney chewed his lip. "Right, well. Last night I ran a full diagnostic of the city's power grid as during the…event…I found out that the explosion had been caused by seemingly random power fluctuations…"

"They began nearly three days ago," Zelenka added, earning himself a glare from Rodney for interrupting. Granted, the scientist caught his look and immediately quieted, but still, an interruption was an interruption.

"Anyway, what I discovered from the diagnostic was that the 'random' fluctuations were not actually random but targeted. There was a virus-like coding in the distribution sub-routine that instructed the city to create several buffers in vital systems in the Central tower, essentially prepping anything with the potential to explode for a catastrophic overload," Rodney looked at the faces around him, not 100% sure that they were following. He decided to simplify it, like he would for Sheppard if he were there. "Worst case scenario, a build-up in the ZedPM console would've have caused an explosion large enough to destroy the entire city."

Lorne let out a low whistle as he appreciated the magnitude of such an explosion, while everyone else at the table paled at the thought of how close they had been to total annihilation. Jennifer gripped his hand tighter under the mahogany table, her eyes wide as she looked at him. Woolsey recovered the fastest, and broke the tense silence. "This virus, is it still a threat?"

"It shouldn't be. I spent all night going through the entire system and I believe that I have completely erased it, but I want to be sure," Rodney replied, but couldn't help adding. "Hence why I haven't reinstalled the ZedPM."

Woolsey threw him a look as if he wanted to retort but felt it would be unprofessional. Instead he settled for asking another question. "Do you know what caused it?"

And this was the part Rodney had been dreading. He didn't know why, he barely knew the culprit, but enough things didn't add up, or rather, added up too well, for him to be completely sold on his conclusion. "It was created and uploaded into the city mainframe using Zelenka's access code to create a back door three days ago. Precisely 83 minutes after the _Apollo_ beamed down the new recruits."

A dark look crossed Lorne's features as he leaned forward. "You're saying that this was intentional sabotage? Who?"

"It's difficult to say for certain," Rodney found himself saying before he realised. Zelenka was giving him that funny look again, as if wondering why Rodney was defending the person essentially responsible for the deaths of fourteen people, plus another fifteen on life support. Rodney couldn't say he knew the answer to that. "But every hacker has a unique way of writing code which makes it possible to identify who it is most likely to have been…"

"Who?" Woolsey asked this time. He didn't look quite as pissed off as Lorne, but his hardened gaze was enough to make Rodney get to the point he was dancing around.

"Miranda McKinley."

* * *

><p><strong>09.00am – Central TowerInfirmary **

"I'm fine, doc…when are you going to let me leave?"

Jennifer gave Colonel Sheppard a stern glare in reply as she busied herself with his chart. The pilot had slept through the night due to his exhaustion and injuries, which was a good thing since that now he was finally been able to talk again he considered himself fit for duty and was ready for one of his prison escapes. She'd have to warn the staff to keep a special eye on him.

"No, Colonel, you are _not_ fine in any sense of the word," she retorted. She was about to list off all of his injuries just to remind him as he seemed to have completely forgotten, but his cocky shrug in reply had ended in a wince, making the reminder unnecessary. "You're better than I expected considering what Lorne has told me, but that doesn't mean that I'm signing you out."

John fixed her with that look of his, the one that told you that he knew what you were really worrying about. Jennifer braced herself. Sometimes the guy's intuition was so on the money it could throw you off completely. "Jennifer, I know you haven't got the resources or the man-power to give everyone here the proper care they need…what if someone goes unnoticed because you're too busy with someone else?"

And there, he'd hit the nail on the head again. She'd already had enough near-misses the night before to remind her of just how unprepared they were for the mass of injured, as well as the poor souls on life support down in the auxiliary med-lab. That morning she had released Lieutenant Henson with his gun-shot wound to the arm purely because she had had no choice, and not because he was ready for light duty.

She had had to call in the night staff early and now all her staff were running after being awake and on duty nearly thirty-six hours. Until the _Daedalus_ arrived with their medical crew she had no-one to relieve her staff. They simply couldn't keep this up – soon they would start making mistakes and in her line of work, mistakes could cost lives.

Jennifer sighed heavily, briefly allowing her exhaustion to show before she hid it behind her professional façade. John gave her a genuinely sympathetic look, but didn't press the issue any further. "Tell you what; I'm going to be allowing everyone who can stand to go to the memorial service tomorrow. If you still seem okay after that, I'll think about releasing you…but not to return to work; not even light duty. Deal?"

John gave her a half-smile. "Deal."

She smiled back, and then tucked his chart away and left him to the small amount of peace he would get before Rodney came by to see him. Her smile collapsed when thinking of Rodney reminded her of the meeting that morning. She still couldn't believe how close they had all been to being completely destroyed – she still couldn't believe it had been on purpose, and that the person responsible was a member of their expedition. Jennifer had never met McKinley, but she had read Lorne's report and knew that she had been instrumental in eradicating the Collective threat. It just didn't make sense.

Jennifer banished the thought from her mind as she continued her rounds, pleased to see that everyone seemed to be improving. She then headed down to the auxiliary infirmary a few floors down to check on…to check on the ones that were sleeping.

Even as a medical professional, it still struck a chord within her when she entered the room to see the masses of tubes covering every patient. The gentle _whoosh-click_ of multiple ventilators hummed in time to each other, the constant beep of heart monitors adding to the rhythm. She was all too aware that it was only the machines that were keeping her patients alive. Their brain activity was zero. Empty shells.

Tears tinged the corners of eyes before she realised that she had stepped in and frozen to the spot. Maria, one of the nurses, gave her a sad smile in acknowledgement before returning her attention to an EKG. Jennifer blinked to clear the tears, and forced herself to move. She walked past the familiar and yet completely alien faces, heading towards the office at the back that Carson had turned into a make-shift lab. She rapped lightly on the door before she entered.

"Jennifer, love," Carson greeted, though there was something off in his voice. She knew what it was. She had read Carson's report as well, the one that was deliberately vague about what had happened in the holding cell, and yet had made it abundantly clear that nothing good had happened. Jennifer wasn't sure what she had done; but she had been there, and now two scientists were dead. He turned away and she knew he was thinking about the same thing.

She couldn't think of anything to say. She felt she should apologise – but she didn't know what for. Instead she started the conversation professionally. "I just came down to see how you were doing. Have you made any progress?"

Carson sighed like a man with the weight of the world on his shoulders. She guessed in a way he was truly carrying the weight of the galaxy as he blamed himself for Michael's experiments with the Hoffan virus, but for once that wasn't why his face was so drawn. "To be terribly honest, I don't believe there is any progress to be made. No matter how hard I try or how much I want there to be some magical cure…"

His voice trailed away. He hadn't looked back at her, and still had yet to meet her eyes. Jennifer respected Carson as a doctor and as a friend. After all they had been through since his return, it hurt her in a way she couldn't describe that he couldn't even bring himself to look at her. Her own words sounded hollow, but they were true. "I'm sorry."

"It's nobody's fault," Carson replied as if she had apologised for his lack of success. They both knew that they were talking about the holding cell. There was long pause following his words, and then he finally turned in his chair. His eyes still didn't quite meet hers, but it was close enough. "I'm going to be taking leave the day after tomorrow, back to Earth."

Jennifer blinked, wondering where that had come from. "I thought you needed to return to M34-J82 to aid the survivors of the Hoffan virus?"

A guilty look passed briefly over Carson's face; it was difficult to distinguish from the one that seemed permanently etched there following his captivity, but she just about caught it. "I should, and I will. But I made a promise to Rowan Fletcher that I intend to keep."

Jennifer recognised the name. Rowan Fletcher was currently lying in their makeshift morgue being prepared for the memorial service the next day. Next to her was Bruno Arrighetti. The pair of them had been found in the holding cell with a distraught Dr. Dharma and Carson after the 'wake up', as it had been dubbed. Again, she found herself lost for words.

"She asked me to be the one to tell her sister what happened, or as much as I can," Carson continued, his eyes clouding with sadness. "Rowan didn't want her to find out through a letter. I'm to tell her that at the end she found happiness, as Bruno Arrighetti finally admitted that he loved her."

Jennifer didn't even try to stop the tears that fell down her cheeks. "I am so, so sorry."

* * *

><p><strong>10.00am – Gamma TowerQuarter Romeo32-K [Provisional Quarters] **

A beep from the door, the equivalent of a knock in Atlantis apparently, brought Miranda McKinley out of her work-induced tunnel vision. She shut the laptop automatically, used to doing top secret work that shouldn't be left on display, and then made the short walk to the door. With a wave of her hand it opened, and she blinked in surprise. "Major Lorne?"

Lorne had a grim expression on his face, and McKinley got the distinct impression it was aimed at her. He stood just outside her door with two soldiers by each shoulder, all of them armed. "I've been ordered to do this privately; mind if we come in?"

_Okay…_McKinley thought to herself, incredibly confused. She stepped aside uncertainly, allowing the three men into her quarters. Part of her was concerned of them seeing the mess she had made in the not-even-three days she had been there, but that part was overwhelmed by the rest of her that was just thinking 'what the hell?' "What is this about?"

She realised then that she was surrounded. One of the soldiers remained by the now-closed door while the other hovered just behind her. Lorne stood before her, the grim expression hidden by a mask of cold professionalism. She was having a strong sense of déjà vu, her mind flashing back to a memory she was pretty sure she'd never forget, no matter how much she wanted to.

"Miranda McKinley…"

It was even the same tone of voice in which he said her name. For the briefest moment, Lorne disappeared and an FBI agent replaced him. _Oh God…not again…_

"…you are to be sent back to Earth immediately where you will be detained pending the result of a full investigation into the deliberate attempt to sabotage and destroy this city." Lorne continued coldly, though his façade slipped a little and she could see the betrayal in his eyes. McKinley suddenly felt empty: as if having her life stolen away once wasn't enough – how many times could she be falsely accused? She didn't even know what she was meant to have done!

"What?" was all she could say. The soldier behind her tensed as if expecting her to try something. Like what? Escape? And just where the hell was she going to go? She had already run to another galaxy to try and get away from her past – how much further was she meant to go?

"There is evidence to suggest that you tampered with the city's computer system; creating a computer virus that caused power problems with the intention of destroying the entire city," Lorne explained, sending McKinley's mind racing. He hadn't used any technical terms; she suspected he hadn't understood the complexities of whatever they had found, but he got the gist. And suddenly everything made sense.

"I didn't do it," she insisted, but knew she wasn't getting through. She knew that Lorne had suffered personally from the events of the day before and was probably glad to have someone else to blame as well as himself. "Look, I designed a code that would do what I think you're describing, but I didn't use it! I would never…it was hypothetical! There were bugs that needed working out, it was never properly completed…and thank God it wasn't…otherwise…"

Her voice trailed off and Lorne fixed her with that grim look again. They were both well aware of what could have happened.

"I didn't do it," McKinley repeated quietly, and she thought that maybe, for less than a millisecond, Lorne almost believed her. She was telling the truth – but that hadn't saved her last time either. "Why would I stay here if I knew I was about to blow everyone up? Why would I try so damn hard to help save the city when the _Alcoloniavarium_ was released? You know this doesn't make sense…please…I didn't do it."

"Lieutenants' Neve and Kilmer will escort you through the Stargate back to the SGC where you will be held while the investigation is undergone," Lorne replied, his expression changing slightly. "You can make a case in your defense then."

_Right, cause that had worked out so well last time._ McKinley just nodded, resigned to once again shouldering a blame that wasn't hers.

She had only made it fifty-two hours in the Pegasus Galaxy – that had to be a record.

* * *

><p><strong>19.00pm – Omega TowerGym Kilo21-G **

When Teyla arrived in the gym she found Ronon beating the living daylights out of a punching bag. The marines that he usually sparred with had wisely found themselves other duties that desperately needed tending to – she doubted they would have fared much better against Ronon in his current mood than the punching bag. He gave it a final punch once he became aware of her presence, and the support wavered dangerously close to giving out. "I thought I would find you here."

Ronon grunted, and then turned his back to her as he pretended to be busy with his gym bag. He pulled out a towel to wipe away the sweat, and then slouched on the bench.

She gestured at the abused gym equipment. "Did it make you feel better?"

"No." His eyes hooded as he took to staring at the floor. She noticed that his knuckles were bloody, but smothered the instinct to go to his side and treat them – she didn't think he would appreciate her fussing over him in his current mood, not that he ever did normally. After a silence where he did everything to avoid meeting her gaze, he muttered. "Did you read the reports?"

Teyla nodded, and then realised he still wasn't looking at her. "Yes, I read both Major Lorne's and Carson's, though I found them both to be deliberately vague on certain details. It is frustrating, but understandable that some things are to be omitted."

"At least you know what you did," Ronon replied shortly. He pushed himself to his feet, grabbing up his stuff as he aimed in the direction of the door. Teyla wouldn't let him retreat that easily though. She purposely stepped into his path, and despite their greatly different heights, stood almost face-to-face with him.

"Yes, I do," she replied a little curtly. "I tried to execute John, threatened my child, held Rodney at gunpoint and then strangled John to within an inch of his life. I was aware and yet powerless throughout – there are moments when I wish I had been oblivious."

Ronon had the sense to look contrite before his eyes darkened again. "It's worse not knowing. You start to read between the lines of what people say, your imagination filling in the gaps. I wish I knew what I had done – at least then I'd know what I was apologizing for."

Teyla placed a hand on his arm, forcing him to meet her eyes. "_We_ didn't do anything – creatures with our faces did those horrible things. We are victims as well, not the culprits. Do you understand?"

"I know that," Ronon muttered quietly. "But it doesn't change a thing. It doesn't make me feel any less guilty."

She nodded, completely understanding. She could still vividly remember wrapping her hands around John's throat. They were _her_ hands, even if it wasn't her actions or intentions. She stepped aside to allow Ronon to pass and then found herself alone in the empty space. She tried listening to her own words to try and lessen the blame she placed on herself, but he was right – logic was never going to change what had happened.

Nothing would ever alleviate the guilt on her heavy heart.

* * *

><p><strong>[Two Days Later] <strong>

**11.00am – Central Tower/Gate Room **

John stood at the bottom of the gate room steps, staring at the table of flags laid out before the Stargate. There simply hadn't been room for all fourteen coffins despite the vastness of the space, so the display served as a memorial for all the lost souls in their place. The coffins would be walked through the gate and back to the SGC later, but for now they were represented with their flags.

Everyone had been affected by the event two days earlier, and as such every member of the expedition had found a way to fit into the gate room, each paying their respects. To John's left stood Lorne, and to his right was Teyla, Torren perched on her hip. Ronon was keeping himself carefully away from Beckett, recognising that he wasn't the scot's favourite person right then – even if he wasn't sure why. Rodney, Dr Keller and Zelenka stood behind John, all of them looking at Woolsey who stood beside the memorial.

Woolsey had never been good at making speeches, but he had managed to pull off something respectful and half-decent without making a fool of himself and unintentionally insulting everyone there. It was more than John thought he could hope for – not that he was volunteering for the job.

"…Sargent Henry Walters, Lieutenant Jaime Harlow, Dr. Rowan Fletcher, Dr Charles Volkov, Dr Leanne Parsons and Dr Bruno Arrighetti: We will never forget."

Woolsey came to an end, and then nodded up at the balcony of the control room where a violinist stood. She took her cue and began a sorrowful melody. All around him John could hear people crying, though in his peripheral vision he could see that neither Lorne nor Teyla were among them. They stood there as rigidly as he did; preventing their emotions from reaching the surface as if such a display would present them as weak. John had never cried at a funeral, not even his mother's. He really hoped that didn't make him a bad person.

The violinist kept playing as the congregation began to scatter. Lorne made no move to leave, and John placed a reassuring hand on his shoulder as he turned. He knew his second-in-command was hurting and that there was nothing he could do to placate it. John saw that Ronon had already slipped away, and Carson had never even acknowledged his presence. He wished he knew what had happened, but he doubted he'd be able to help regardless.

There were some wounds that would just never heal.

* * *

><p><strong>[Three Days Later] <strong>

**14.00pm – Gamma Tower/Quarter Alpha83-F [Sheppard's Quarters] **

The moment the door opened, Teyla forgot all the carefully constructed things that she had been planning to say. Instead, she found herself declaring "You've been avoiding me, John."

He stepped back from the door with a guilty expression and walked over to his bed, his back to her. She took the open door as an invitation and stepped inside, allowing it to close behind her. It was then that she noticed the bag on his bed, a pile of folded clothes next to it just waiting to be packed. "Are you going somewhere?"

John picked up a pile with one hand – his right arm trapped in a sling – and haphazardly shoved it into the duffel. Even from the distance between them she could see that his movements were stilted, his injuries causing him pain every time they were jostled. "Yeah," he answered, still not turning to face her. "I'm going to be taking leave on Earth for a while. Lorne needs the support even if he isn't asking for it."

Teyla couldn't help the pang of annoyance that ran through her. She knew he was running away, and she suspected it was from her. They hadn't really spoken since the kiss…when she had gone to see him in the infirmary he hadn't even been able to talk, and he'd been skilfully avoiding her since. "Were you going to tell me?"

"Of course, I just…" he trailed off, realising he had run out of things to pack. He failed at zipping the bag up one-handed, so Teyla stepped in to help. This close, he couldn't avoid looking at her, and she could see the confusion in his eyes. She imagined that an unexplained kiss from nowhere would do that - even she was confused over its meaning, and she had been the one to instigate it. They had been friends for such a long time, was it even possible at this point for them to become something more?

"John…" Teyla began, trying to find the right words. She had unconsciously placed a hand on his arm, and she was pleased to find that he didn't shy away. "About…about the kiss. I know it was sudden, and a little impulsive…but I…it was true. I won't apologise."

John studied her then, guarded hope in his eyes as if he couldn't quite allow himself to believe her. And then a shadow crossed his features. "What about Kanaan? And Torren?"

"Kanaan…understands," Teyla replied; she thought back to her visit a few days ago, the guilt still heavy on her already laden conscience. "We have been drifting apart for some time now; I'm not even sure if we were ever truly together. And Torren…Torren will know his father regardless of whether we are joined or not."

"It could make things…complicated," John said after a moment. Teyla gave him a smile, and then she reached up and kissed him again. This time there was no hesitation from him, his hand settling on her waist as he returned her kiss.

Eventually, she pulled back, but looked up at him with the same smile. "I think we can handle 'complicated'."

* * *

><p><strong>15.00pm – Central TowerGate Room **

Lorne stared at the inactive gate with more than a little trepidation. Woolsey had granted him his leave despite the fact that, for the time being at least, there was no military commander on Atlantis. Caldwell was en-route in the _Daedalus_ though, and since being apprised of the situation, had offered to stand in when he arrived. It meant that Lorne had no excuse for not going to Earth now – not that he wanted to back out – but he couldn't say he was looking forward to it. He hoped that made him normal.

He stood alone for a few minutes before Colonel Sheppard appeared from nowhere next to him, depositing his own duffel bag next to Lorne's. He gave Sheppard an uncertain glance. "Sir?"

"No one should find out in a letter, major," was all Sheppard said in reply, staring straight ahead as he said it. Lorne nodded. He strongly suspected that his CO was there for him as well as to visit the families of the fallen soldiers, and for that he was immensely grateful. There was nothing worse than being the one tell someone that they had lost a loved one; at least Lorne wouldn't be doing it alone.

Less than a minute passed before McKay came to join them, a laptop tucked under one arm and his bag in the other. Lorne gave him a questioning look.

"The SGC has asked that I present my findings directly to the IOA," he gestured his laptop. "Apparently they want to wrap this up as quickly as possible, and having someone to point the finger at makes things a lot easier."

McKay still didn't look entirely convinced that McKinley was the one responsible, and after confronting her two days earlier, Lorne was finding it difficult to believe as well. The idea that someone else had tried and was walking around free unnerved him greatly. What was to stop them from trying again? He would launch his own investigation once he returned, even if McKinley _was_ found guilty. Even he could see how things didn't add up right.

They stood in silence for a while before Dr Beckett came to join them. There was no need to ask what he was doing there; they had read his report – and between the lines of it.

It was then that Chuck dialled the Stargate, the lights around the ring spinning in sequence until the gate locked, the wormhole initiating with its spectacular_ kawoosh_. Once it settled into place, the four of them walked forward and disappeared into the serene pool of blue.

* * *

><p><strong>There! All finished now! Really hope that you have enjoyed reading this as much as I have had fun writing it! And thank you in advance to future reviewers – if the count gets above 100 I will actually die dancing like a maniac with hysterical happiness, film it, and then put it on YouTube (…from the grave…)<strong>

**Hopefully, however, I will then return from the dead so that I can write the next fic that is just begging to be written :P Because I'm an opportunist, I am once again going to advertise the not-even-planned fic right here:**

**Summary:** Sheppard and the team step through the gate…and into the middle of a warzone. As Prisoners of War they find themselves trapped not only by their captors, but by the very planet as it falls apart around them…

_Action/Adventure/Hurt/Comfort, Set Season 4 (Carter leader/pre-Teyla pregnancy) No Pairings, and most importantly – Shepwhump a-plenty_

'**Endgame' – coming to fanfic site near you! (Or you know…the web, which is local to anyone with an internet connection…) Hopefully see you then!**


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